From 4f19436d51be0a9e278183663d1dec3c1700f30d Mon Sep 17 00:00:00 2001
From: ielis <daniel.gordon.danis@protonmail.com>
Date: Fri, 13 Sep 2024 19:13:01 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20monarch-?=
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---
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 .../gpsea.analysis.predicate.genotype.html    |   1 -
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 latest/apidocs/gpsea.analysis.pscore.html     |   1 -
 .../apidocs/gpsea.analysis.pscore.stats.html  |   5 +-
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 latest/apidocs/gpsea.html                     |   2 -
 latest/apidocs/gpsea.model.genome.html        |   1 -
 latest/apidocs/gpsea.model.html               |   5 +-
 latest/apidocs/gpsea.preprocessing.html       |   1 -
 latest/apidocs/gpsea.view.html                |   1 -
 latest/genindex.html                          |   9 -
 latest/objects.inv                            | Bin 6956 -> 6936 bytes
 latest/py-modindex.html                       |   5 -
 latest/searchindex.js                         |   2 +-
 .../gpsea/analysis/mtc_filter/_impl.html      | 259 ++++--
 .../_modules/gpsea/analysis/pcats/_impl.html  | 145 +--
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 .../predicate/genotype/_gt_predicates.html    | 607 ++++++-------
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 .../analysis/predicate/phenotype/_pheno.html  |  48 +-
 .../analysis/predicate/phenotype/_util.html   |  10 +-
 .../_modules/gpsea/analysis/pscore/_api.html  |   6 +-
 .../_modules/gpsea/analysis/pscore/_impl.html |   6 +-
 .../gpsea/analysis/pscore/stats/_stats.html   |   6 +-
 stable/_modules/gpsea/config.html             |   6 +-
 stable/_modules/gpsea/data/_toy.html          | 430 ---------
 stable/_modules/gpsea/io.html                 |   6 +-
 stable/_modules/gpsea/model/_base.html        |   6 +-
 stable/_modules/gpsea/model/_cohort.html      |   6 +-
 stable/_modules/gpsea/model/_gt.html          |   6 +-
 stable/_modules/gpsea/model/_phenotype.html   |   6 +-
 stable/_modules/gpsea/model/_protein.html     |   6 +-
 stable/_modules/gpsea/model/_tx.html          |   6 +-
 stable/_modules/gpsea/model/_variant.html     |   6 +-
 .../gpsea/model/_variant_effects.html         | 109 ++-
 .../_modules/gpsea/model/genome/_genome.html  |   6 +-
 stable/_modules/gpsea/preprocessing/_api.html |   6 +-
 .../_modules/gpsea/preprocessing/_audit.html  |   6 +-
 .../_modules/gpsea/preprocessing/_config.html |   8 +-
 .../gpsea/preprocessing/_generic.html         |   6 +-
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 .../gpsea/preprocessing/_phenotype.html       |   6 +-
 .../gpsea/preprocessing/_protein.html         |   6 +-
 .../gpsea/preprocessing/_uniprot.html         |  92 +-
 .../gpsea/preprocessing/_variant.html         |   6 +-
 stable/_modules/gpsea/preprocessing/_vep.html |   6 +-
 stable/_modules/gpsea/preprocessing/_vv.html  |   6 +-
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 .../gpsea/view/_cohort_variant_viewer.html    | 277 ++++++
 stable/_modules/gpsea/view/_disease.html      |   6 +-
 stable/_modules/gpsea/view/_formatter.html    |   6 +-
 .../gpsea/view/_phenotype_analysis.html       | 192 ++++
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 .../gpsea/view/_protein_visualizable.html     |   6 +-
 .../gpsea/view/_protein_visualizer.html       |   6 +-
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 stable/_modules/gpsea/view/_txp.html          |   6 +-
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 stable/_sources/apidocs/gpsea.rst.txt         |   1 -
 stable/_sources/index.rst.txt                 |   4 +-
 stable/_sources/tutorial.rst.txt              |  67 +-
 stable/_sources/user-guide/index.rst.txt      |   9 +-
 stable/_sources/user-guide/input-data.rst.txt |   2 +-
 stable/_sources/user-guide/mtc.rst.txt        | 150 ++--
 stable/_sources/user-guide/predicates.rst.txt | 497 +----------
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 .../predicates/genotype_predicates.rst.txt    |  32 +
 .../predicates/groups_predicate.rst.txt       |  41 +
 .../predicates/hpo_predicate.rst.txt          |  87 ++
 .../predicates/male_female_predicate.rst.txt  |  21 +
 .../mode_of_inheritance_predicate.rst.txt     |  93 ++
 .../phenotype_predicates.rst.txt              |   1 +
 .../predicates/variant_predicates.rst.txt     | 168 ++++
 stable/_sources/user-guide/stats.rst.txt      |  27 +-
 stable/_static/documentation_options.js       |   2 +-
 stable/apidocs/gpsea.analysis.html            |   8 +-
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 .../apidocs/gpsea.analysis.pcats.stats.html   |   7 +-
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 stable/apidocs/gpsea.data.html                | 142 ---
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 stable/genindex.html                          | 150 ++--
 stable/index.html                             |  10 +-
 stable/installation.html                      |   6 +-
 stable/objects.inv                            | Bin 6542 -> 6936 bytes
 stable/py-modindex.html                       |  11 +-
 stable/search.html                            |   6 +-
 stable/searchindex.js                         |   2 +-
 stable/tutorial.html                          | 823 +++++++++++++++---
 stable/user-guide/autosomal_recessive.html    |   7 +-
 stable/user-guide/exploratory.html            |   7 +-
 stable/user-guide/general_hpo_terms.html      |   6 +-
 stable/user-guide/glossary.html               |   7 +-
 stable/user-guide/index.html                  |  13 +-
 stable/user-guide/input-data.html             |   9 +-
 stable/user-guide/mtc.html                    | 111 +--
 stable/user-guide/phenotype_predicates.html   | 143 ---
 stable/user-guide/predicates.html             | 516 +----------
 .../user-guide/{ => predicates}/devries.html  |  95 +-
 .../predicates/diagnosis_predicate.html       | 161 ++++
 .../predicates/genotype_predicates.html       | 167 ++++
 .../predicates/groups_predicate.html          | 175 ++++
 .../user-guide/predicates/hpo_predicate.html  | 215 +++++
 .../predicates/male_female_predicate.html     | 158 ++++
 .../mode_of_inheritance_predicate.html        | 241 +++++
 .../predicates/phenotype_predicates.html      | 153 ++++
 .../predicates/variant_predicates.html        | 305 +++++++
 stable/user-guide/stats.html                  | 201 ++---
 133 files changed, 4937 insertions(+), 3368 deletions(-)
 delete mode 100644 latest/_sources/apidocs/gpsea.data.rst.txt
 delete mode 100644 latest/apidocs/gpsea.data.html
 delete mode 100644 stable/_modules/gpsea/data/_toy.html
 create mode 100644 stable/_modules/gpsea/view/_cohort_variant_viewer.html
 create mode 100644 stable/_modules/gpsea/view/_phenotype_analysis.html
 delete mode 100644 stable/_sources/apidocs/gpsea.data.rst.txt
 rename stable/_sources/user-guide/{ => predicates}/devries.rst.txt (100%)
 create mode 100644 stable/_sources/user-guide/predicates/diagnosis_predicate.rst.txt
 create mode 100644 stable/_sources/user-guide/predicates/genotype_predicates.rst.txt
 create mode 100644 stable/_sources/user-guide/predicates/groups_predicate.rst.txt
 create mode 100644 stable/_sources/user-guide/predicates/hpo_predicate.rst.txt
 create mode 100644 stable/_sources/user-guide/predicates/male_female_predicate.rst.txt
 create mode 100644 stable/_sources/user-guide/predicates/mode_of_inheritance_predicate.rst.txt
 rename stable/_sources/user-guide/{ => predicates}/phenotype_predicates.rst.txt (94%)
 create mode 100644 stable/_sources/user-guide/predicates/variant_predicates.rst.txt
 delete mode 100644 stable/apidocs/gpsea.data.html
 delete mode 100644 stable/user-guide/phenotype_predicates.html
 rename stable/user-guide/{ => predicates}/devries.html (75%)
 create mode 100644 stable/user-guide/predicates/diagnosis_predicate.html
 create mode 100644 stable/user-guide/predicates/genotype_predicates.html
 create mode 100644 stable/user-guide/predicates/groups_predicate.html
 create mode 100644 stable/user-guide/predicates/hpo_predicate.html
 create mode 100644 stable/user-guide/predicates/male_female_predicate.html
 create mode 100644 stable/user-guide/predicates/mode_of_inheritance_predicate.html
 create mode 100644 stable/user-guide/predicates/phenotype_predicates.html
 create mode 100644 stable/user-guide/predicates/variant_predicates.html

diff --git a/latest/_sources/apidocs/gpsea.data.rst.txt b/latest/_sources/apidocs/gpsea.data.rst.txt
deleted file mode 100644
index 2940ee0e8..000000000
--- a/latest/_sources/apidocs/gpsea.data.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-gpsea.data package
-==================
-
-.. automodule:: gpsea.data
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/latest/_sources/apidocs/gpsea.rst.txt b/latest/_sources/apidocs/gpsea.rst.txt
index 69d0030f8..ba30e3729 100644
--- a/latest/_sources/apidocs/gpsea.rst.txt
+++ b/latest/_sources/apidocs/gpsea.rst.txt
@@ -13,7 +13,6 @@ Subpackages
    :maxdepth: 2
 
    gpsea.analysis
-   gpsea.data
    gpsea.model
    gpsea.preprocessing
    gpsea.view
diff --git a/latest/apidocs/gpsea.analysis.html b/latest/apidocs/gpsea.analysis.html
index 4eb521b07..7c90e304f 100644
--- a/latest/apidocs/gpsea.analysis.html
+++ b/latest/apidocs/gpsea.analysis.html
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
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 <li class="toctree-l4 current"><a class="current reference internal" href="#">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.mtc_filter.html b/latest/apidocs/gpsea.analysis.mtc_filter.html
index ee5bbdd43..6ad984bfd 100644
--- a/latest/apidocs/gpsea.analysis.mtc_filter.html
+++ b/latest/apidocs/gpsea.analysis.mtc_filter.html
@@ -62,7 +62,6 @@
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 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.pcats.html b/latest/apidocs/gpsea.analysis.pcats.html
index a6e17296a..d643c538f 100644
--- a/latest/apidocs/gpsea.analysis.pcats.html
+++ b/latest/apidocs/gpsea.analysis.pcats.html
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.pcats.stats.html b/latest/apidocs/gpsea.analysis.pcats.stats.html
index b8cf253e1..7dd077a09 100644
--- a/latest/apidocs/gpsea.analysis.pcats.stats.html
+++ b/latest/apidocs/gpsea.analysis.pcats.stats.html
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.predicate.genotype.html b/latest/apidocs/gpsea.analysis.predicate.genotype.html
index 12aeb7ff1..6ff161b93 100644
--- a/latest/apidocs/gpsea.analysis.predicate.genotype.html
+++ b/latest/apidocs/gpsea.analysis.predicate.genotype.html
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.predicate.html b/latest/apidocs/gpsea.analysis.predicate.html
index f38563a01..4189d7ee8 100644
--- a/latest/apidocs/gpsea.analysis.predicate.html
+++ b/latest/apidocs/gpsea.analysis.predicate.html
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.predicate.phenotype.html b/latest/apidocs/gpsea.analysis.predicate.phenotype.html
index 3b8c55149..46beaf19c 100644
--- a/latest/apidocs/gpsea.analysis.predicate.phenotype.html
+++ b/latest/apidocs/gpsea.analysis.predicate.phenotype.html
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.pscore.html b/latest/apidocs/gpsea.analysis.pscore.html
index 2b861c05d..44618624b 100644
--- a/latest/apidocs/gpsea.analysis.pscore.html
+++ b/latest/apidocs/gpsea.analysis.pscore.html
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/latest/apidocs/gpsea.analysis.pscore.stats.html b/latest/apidocs/gpsea.analysis.pscore.stats.html
index 48c6ad1f3..70c955a0a 100644
--- a/latest/apidocs/gpsea.analysis.pscore.stats.html
+++ b/latest/apidocs/gpsea.analysis.pscore.stats.html
@@ -25,7 +25,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="gpsea.data package" href="gpsea.data.html" />
+    <link rel="next" title="gpsea.model package" href="gpsea.model.html" />
     <link rel="prev" title="gpsea.analysis.pscore package" href="gpsea.analysis.pscore.html" /> 
 </head>
 
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -153,7 +152,7 @@
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="gpsea.analysis.pscore.html" class="btn btn-neutral float-left" title="gpsea.analysis.pscore package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="gpsea.data.html" class="btn btn-neutral float-right" title="gpsea.data package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="gpsea.model.html" class="btn btn-neutral float-right" title="gpsea.model package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/latest/apidocs/gpsea.data.html b/latest/apidocs/gpsea.data.html
deleted file mode 100644
index 0b37efda0..000000000
--- a/latest/apidocs/gpsea.data.html
+++ /dev/null
@@ -1,137 +0,0 @@
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-<html class="writer-html5" lang="en" data-content_root="../">
-<head>
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-
-  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.data package &mdash; GPSEA 0.3.1.dev0 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
-      <link rel="stylesheet" type="text/css" href="../_static/gpsea.css?v=547657ed" />
-
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-    <script src="../_static/js/html5shiv.min.js"></script>
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diff --git a/latest/apidocs/gpsea.html b/latest/apidocs/gpsea.html
index 8aa74809a..a53c1be5c 100644
--- a/latest/apidocs/gpsea.html
+++ b/latest/apidocs/gpsea.html
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="current reference internal" href="#">gpsea package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#subpackages">Subpackages</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
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 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -115,7 +114,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
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 <li class="toctree-l1"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a><ul>
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 <li class="toctree-l2"><a class="reference internal" href="gpsea.model.html#gpsea.model.Patient"><code class="docutils literal notranslate"><span class="pre">Patient</span></code></a></li>
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diff --git a/latest/apidocs/gpsea.model.html b/latest/apidocs/gpsea.model.html
index e4ea538f9..661d6084a 100644
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@@ -1688,7 +1687,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
            </div>
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diff --git a/latest/apidocs/gpsea.preprocessing.html b/latest/apidocs/gpsea.preprocessing.html
index c81034a72..135cfc890 100644
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diff --git a/latest/apidocs/gpsea.view.html b/latest/apidocs/gpsea.view.html
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diff --git a/latest/py-modindex.html b/latest/py-modindex.html
index 20ca97002..146eacd88 100644
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+++ b/latest/py-modindex.html
@@ -149,11 +149,6 @@ <h1>Python Module Index</h1>
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-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="apidocs/gpsea.data.html#module-gpsea.data"><code class="xref">gpsea.data</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
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        <td>&#160;&#160;&#160;
diff --git a/latest/searchindex.js b/latest/searchindex.js
index 7fcfffd10..cfc1cf331 100644
--- a/latest/searchindex.js
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\ No newline at end of file
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\ No newline at end of file
diff --git a/stable/_modules/gpsea/analysis/mtc_filter/_impl.html b/stable/_modules/gpsea/analysis/mtc_filter/_impl.html
index 639c81395..8ca0e6160 100644
--- a/stable/_modules/gpsea/analysis/mtc_filter/_impl.html
+++ b/stable/_modules/gpsea/analysis/mtc_filter/_impl.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.mtc_filter._impl &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.mtc_filter._impl &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../_static/documentation_options.js?v=6c02275b"></script>
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         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
@@ -82,12 +82,12 @@
              
   <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">abc</span>
+<span class="kn">import</span> <span class="nn">dataclasses</span>
 <span class="kn">import</span> <span class="nn">typing</span>
 
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">deque</span>
 
 <span class="kn">import</span> <span class="nn">hpotk</span>
-<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">axis</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 
@@ -95,6 +95,26 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="kn">from</span> <span class="nn">..predicate.phenotype</span> <span class="kn">import</span> <span class="n">PhenotypePolyPredicate</span><span class="p">,</span> <span class="n">P</span>
 
 
+<div class="viewcode-block" id="PhenotypeMtcIssue">
+<a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcIssue">[docs]</a>
+<span class="nd">@dataclasses</span><span class="o">.</span><span class="n">dataclass</span><span class="p">(</span><span class="n">eq</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">frozen</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<span class="k">class</span> <span class="nc">PhenotypeMtcIssue</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    The container for data available regarding the reason why a phenotype was filtered out.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">code</span><span class="p">:</span> <span class="nb">str</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    A `str` with a unique code of the issue.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    
+    <span class="n">reason</span><span class="p">:</span> <span class="nb">str</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    A human-friendly explanation of the issue.</span>
+<span class="sd">    &quot;&quot;&quot;</span></div>
+
+
+
 <div class="viewcode-block" id="PhenotypeMtcResult">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult">[docs]</a>
 <span class="k">class</span> <span class="nc">PhenotypeMtcResult</span><span class="p">:</span>
@@ -102,7 +122,8 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">    `PhenotypeMtcResult` represents a result of :class:`PhenotypeMtcFilter` for a single phenotype.</span>
 
 <span class="sd">    The phenotype can either pass the filter, in order to be included in the downstream analysis (:meth:`is_passed`)</span>
-<span class="sd">    of be filtered out (:meth:`is_filtered_out`) in which case :attr:`reason` must be available.</span>
+<span class="sd">    of be filtered out (:meth:`is_filtered_out`) in which case :attr:`mtc_issue` with more context</span>
+<span class="sd">    regarding the culprit must be available.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
 <div class="viewcode-block" id="PhenotypeMtcResult.ok">
@@ -110,23 +131,30 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
     <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">ok</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="s2">&quot;PhenotypeMtcResult&quot;</span><span class="p">:</span>
         <span class="c1"># A singleton would be nice here...</span>
-        <span class="k">return</span> <span class="n">PhenotypeMtcResult</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">reason</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">PhenotypeMtcResult</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">issue</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="PhenotypeMtcResult.fail">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.fail">[docs]</a>
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">fail</span><span class="p">(</span><span class="n">reason</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;PhenotypeMtcResult&quot;</span><span class="p">:</span>
-        <span class="k">return</span> <span class="n">PhenotypeMtcResult</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">reason</span><span class="o">=</span><span class="n">reason</span><span class="p">)</span></div>
+    <span class="k">def</span> <span class="nf">fail</span><span class="p">(</span><span class="n">code</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">reason</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;PhenotypeMtcResult&quot;</span><span class="p">:</span>
+        <span class="n">issue</span> <span class="o">=</span> <span class="n">PhenotypeMtcIssue</span><span class="p">(</span><span class="n">code</span><span class="o">=</span><span class="n">code</span><span class="p">,</span> <span class="n">reason</span><span class="o">=</span><span class="n">reason</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">PhenotypeMtcResult</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">issue</span><span class="o">=</span><span class="n">issue</span><span class="p">)</span></div>
 
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">status</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
-        <span class="n">reason</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">issue</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">PhenotypeMtcIssue</span><span class="p">],</span>
     <span class="p">):</span>
+        <span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">status</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">status</span><span class="p">:</span>
+            <span class="k">assert</span> <span class="n">issue</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">&#39;`issue` must NOT be provided if the HPO term passed the MTC filter&#39;</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">assert</span> <span class="n">issue</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">&#39;`issue` must be provided if the HPO term failed the MTC filter&#39;</span>
+        
         <span class="bp">self</span><span class="o">.</span><span class="n">_status</span> <span class="o">=</span> <span class="n">status</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_reason</span> <span class="o">=</span> <span class="n">reason</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_issue</span> <span class="o">=</span> <span class="n">issue</span>
 
 <div class="viewcode-block" id="PhenotypeMtcResult.is_passed">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_passed">[docs]</a>
@@ -139,21 +167,28 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
     <span class="k">def</span> <span class="nf">is_filtered_out</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
         <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_status</span></div>
 
-    
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">mtc_issue</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">PhenotypeMtcIssue</span><span class="p">]:</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_issue</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">reason</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_reason</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">mtc_issue</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">mtc_issue</span><span class="o">.</span><span class="n">reason</span>
     
     <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
         <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">PhenotypeMtcResult</span><span class="p">)</span> \
             <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_status</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_status</span> \
-            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_reason</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_reason</span>
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_issue</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_issue</span>
 
     <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
-        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">_status</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_reason</span><span class="p">))</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">_status</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_issue</span><span class="p">))</span>
     
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="sa">f</span><span class="s1">&#39;PhenotypeMtcResult(status=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_status</span><span class="si">}</span><span class="s1">, reason=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_reason</span><span class="si">}</span><span class="s1">)&#39;</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s1">&#39;PhenotypeMtcResult(status=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_status</span><span class="si">}</span><span class="s1">, issue=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_issue</span><span class="si">}</span><span class="s1">)&#39;</span>
     
     <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
         <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
@@ -171,6 +206,14 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">    Therefore, the expected input asks for :class:`hpotk.TermId` items.</span>
 <span class="sd">    For instance, `n_usable` is a mapping from an *HPO term* to an `int` with the count of the patients</span>
 <span class="sd">    categorized according to the HPO term.</span>
+
+<span class="sd">    :attr:`PhenotypeMtcFilter.OK` is returned for HPO terms that pass MTC filtering</span>
+<span class="sd">    and *should* be included in the analysis.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">OK</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">ok</span><span class="p">()</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    The MTC result for the phenotypes that pass the filtering and *should* be included in the analysis.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
 <div class="viewcode-block" id="PhenotypeMtcFilter.filter">
@@ -194,6 +237,16 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
         <span class="k">pass</span></div>
 
 
+<div class="viewcode-block" id="PhenotypeMtcFilter.possible_results">
+<a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.possible_results">[docs]</a>
+    <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
+    <span class="k">def</span> <span class="nf">possible_results</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Collection</span><span class="p">[</span><span class="n">PhenotypeMtcResult</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Return all possible result types which the `PhenotypeMtcFilter` can produce.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">pass</span></div>
+
+
 <div class="viewcode-block" id="PhenotypeMtcFilter.filter_method_name">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter_method_name">[docs]</a>
     <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
@@ -215,9 +268,6 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">    See :ref:`use-all-terms-strategy` section for more info.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_ok</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">ok</span><span class="p">()</span>
-
 <div class="viewcode-block" id="UseAllTermsMtcFilter.filter">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter">[docs]</a>
     <span class="k">def</span> <span class="nf">filter</span><span class="p">(</span>
@@ -227,7 +277,13 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
         <span class="n">counts</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">],</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">PhenotypeMtcResult</span><span class="p">]:</span>
         <span class="c1"># Always OK! 😏</span>
-        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_ok</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">ph_predicates</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">PhenotypeMtcFilter</span><span class="o">.</span><span class="n">OK</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">ph_predicates</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="UseAllTermsMtcFilter.possible_results">
+<a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.possible_results">[docs]</a>
+    <span class="k">def</span> <span class="nf">possible_results</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Collection</span><span class="p">[</span><span class="n">PhenotypeMtcResult</span><span class="p">]:</span>
+        <span class="k">return</span> <span class="p">(</span><span class="n">PhenotypeMtcFilter</span><span class="o">.</span><span class="n">OK</span><span class="p">,)</span></div>
 
 
 <div class="viewcode-block" id="UseAllTermsMtcFilter.filter_method_name">
@@ -250,6 +306,11 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">    being tested and reducing the multiple testing burden.</span>
 <span class="sd">    </span>
 <span class="sd">    See :ref:`specify-terms-strategy` section for more info.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    
+    <span class="n">NON_SPECIFIED_TERM</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="n">code</span><span class="o">=</span><span class="s2">&quot;ST1&quot;</span><span class="p">,</span> <span class="n">reason</span><span class="o">=</span><span class="s2">&quot;Non-specified term&quot;</span><span class="p">)</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    The MTC filtering result returned when an HPO term does not belong among the selection of terms to be tested.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
@@ -260,8 +321,6 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">        Args:</span>
 <span class="sd">            terms_to_test: an iterable of TermIds representing the terms to test</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_ok</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">ok</span><span class="p">()</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_fail</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="s2">&quot;Non-specified term&quot;</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_terms_to_test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">terms_to_test</span><span class="p">)</span>
 
 <div class="viewcode-block" id="SpecifiedTermsMtcFilter.filter">
@@ -275,11 +334,20 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
         <span class="n">results</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="k">for</span> <span class="n">predicate</span> <span class="ow">in</span> <span class="n">ph_predicates</span><span class="p">:</span>
             <span class="k">if</span> <span class="n">predicate</span><span class="o">.</span><span class="n">phenotype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_terms_to_test_set</span><span class="p">:</span>
-                <span class="n">results</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_ok</span><span class="p">)</span>
+                <span class="n">results</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">SpecifiedTermsMtcFilter</span><span class="o">.</span><span class="n">OK</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
-                <span class="n">results</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_fail</span><span class="p">)</span>
+                <span class="n">results</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">SpecifiedTermsMtcFilter</span><span class="o">.</span><span class="n">NON_SPECIFIED_TERM</span><span class="p">)</span>
         <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">results</span><span class="p">)</span></div>
 
+    
+<div class="viewcode-block" id="SpecifiedTermsMtcFilter.possible_results">
+<a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.possible_results">[docs]</a>
+    <span class="k">def</span> <span class="nf">possible_results</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Collection</span><span class="p">[</span><span class="n">PhenotypeMtcResult</span><span class="p">]:</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">PhenotypeMtcFilter</span><span class="o">.</span><span class="n">OK</span><span class="p">,</span>
+            <span class="n">SpecifiedTermsMtcFilter</span><span class="o">.</span><span class="n">NON_SPECIFIED_TERM</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
 
 <div class="viewcode-block" id="SpecifiedTermsMtcFilter.filter_method_name">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter_method_name">[docs]</a>
@@ -301,16 +369,21 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">    We recommend creating an instance using the :func:`default_filter` static factory method.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="c1"># TODO: this has been here before. Is it still valid?</span>
-    <span class="c1"># 2. Do not perform a test if the counts in the genotype categories do not even have nominal statistical power</span>
-    <span class="c1"># for i in range(2,6):</span>
-    <span class="c1">#     for j in range(2,6):</span>
-    <span class="c1">#         # create a table with the most extreme possible counts. If this is not significant, then</span>
-    <span class="c1">#         # other counts also cannot be</span>
-    <span class="c1">#         two_by_two_table = [[i, 0], [0, j]]</span>
-    <span class="c1">#         oddsr, p = scipy.stats.fisher_exact(two_by_two_table, alternative=&#39;two-sided&#39;)</span>
-    <span class="c1"># This code reveals that (2,4), (4,2), (2,3), (3,3), (2,2) and (3,2) are not powered so we can always skip them</span>
-    <span class="c1"># ## TODO -- similar calculate for 3x2</span>
+    <span class="n">NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+        <span class="s2">&quot;HMF02&quot;</span><span class="p">,</span> <span class="s2">&quot;Skipping term because no genotype has more than one observed HPO count&quot;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">SAME_COUNT_AS_THE_ONLY_CHILD</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+        <span class="s2">&quot;HMF03&quot;</span><span class="p">,</span> <span class="s2">&quot;Skipping term because of a child term with the same individual counts&quot;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">SKIPPING_SAME_OBSERVED_PROPORTIONS</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+        <span class="s2">&quot;HMF04&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;Skipping term because all genotypes have same HPO observed proportions&quot;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+        <span class="s2">&quot;HMF05&quot;</span><span class="p">,</span> <span class="s2">&quot;Skipping term because one genotype had zero observations&quot;</span>
+    <span class="p">)</span>
+    <span class="n">SKIPPING_NON_PHENOTYPE_TERM</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="s2">&quot;HMF07&quot;</span><span class="p">,</span> <span class="s2">&quot;Skipping non phenotype term&quot;</span><span class="p">)</span>
+    <span class="n">SKIPPING_GENERAL_TERM</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="s2">&quot;HMF08&quot;</span><span class="p">,</span> <span class="s2">&quot;Skipping general term&quot;</span><span class="p">)</span>
 
 <div class="viewcode-block" id="HpoMtcFilter.default_filter">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter">[docs]</a>
@@ -392,13 +465,40 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_hpo</span> <span class="o">=</span> <span class="n">hpo</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_hpo_term_frequency_filter</span> <span class="o">=</span> <span class="n">term_frequency_threshold</span>
-        <span class="c1"># The following numbers of total observations in the genotype groups can never be significant,</span>
-        <span class="c1"># so we just skip them see above explanation</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_powerless_set</span> <span class="o">=</span> <span class="p">{(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">),</span> <span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">)}</span>
-        <span class="c1"># thus if the total count is 6 or less, there is no power - CAN WE SIMPLIFY?</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">_general_hpo_terms</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">general_hpo_terms</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_ok</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">ok</span><span class="p">()</span>
+        
+        <span class="bp">self</span><span class="o">.</span><span class="n">_below_frequency_threshold</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+            <span class="n">code</span><span class="o">=</span><span class="s2">&quot;HMF01&quot;</span><span class="p">,</span>
+            <span class="n">reason</span><span class="o">=</span><span class="s2">&quot;Skipping term with maximum frequency that was&quot;</span>
+            <span class="sa">f</span><span class="s2">&quot; less than threshold </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_hpo_term_frequency_filter</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Do not perform a test if the counts in the genotype categories do not even have nominal statistical power</span>
+        <span class="c1"># The following numbers of total observations in the genotype groups can never be significant,</span>
+        <span class="c1"># so we just skip them.</span>
+        <span class="c1"># ```</span>
+        <span class="c1"># for i in range(2,6):</span>
+        <span class="c1">#     for j in range(2,6):</span>
+        <span class="c1">#         # create a table with the most extreme possible counts. If this is not significant, then</span>
+        <span class="c1">#         # other counts also cannot be</span>
+        <span class="c1">#         two_by_two_table = [[i, 0], [0, j]]</span>
+        <span class="c1">#         oddsr, p = scipy.stats.fisher_exact(two_by_two_table, alternative=&#39;two-sided&#39;)</span>
+        <span class="c1"># ```</span>
+        <span class="c1"># This code reveals that (2,4), (4,2), (2,3), (3,3), (2,2) and (3,2) are not powered so we can always skip them</span>
+        <span class="c1"># Thus if the total count is 6 or less, there is no power.</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_min_observations_for_2_by_2</span> <span class="o">=</span> <span class="mi">7</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_not_powered_for_2_by_2</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+            <span class="n">code</span><span class="o">=</span><span class="s2">&quot;HMF06&quot;</span><span class="p">,</span>
+            <span class="n">reason</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Skipping term with less than </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_min_observations_for_2_by_2</span><span class="si">}</span><span class="s2"> observations&quot;</span>
+            <span class="s2">&quot; (not powered for 2x2)&quot;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_min_observations_for_2_by_3</span> <span class="o">=</span> <span class="mi">6</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_not_powered_for_2_by_3</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span>
+            <span class="n">code</span><span class="o">=</span><span class="s2">&quot;HMF06&quot;</span><span class="p">,</span>
+            <span class="n">reason</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Skipping term with less than </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_min_observations_for_2_by_3</span><span class="si">}</span><span class="s2"> observations&quot;</span>
+            <span class="s2">&quot; (not powered for 2x3)&quot;</span><span class="p">,</span>
+        <span class="p">)</span>
 
 <div class="viewcode-block" id="HpoMtcFilter.filter">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.filter">[docs]</a>
@@ -422,46 +522,39 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
                 <span class="k">continue</span>
 
             <span class="k">if</span> <span class="n">term_id</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_general_hpo_terms</span><span class="p">:</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="s2">&quot;Skipping general term&quot;</span><span class="p">)</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_GENERAL_TERM</span>
                 <span class="k">continue</span>
             
             <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hpo</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">is_ancestor_of</span><span class="p">(</span>
                 <span class="n">hpotk</span><span class="o">.</span><span class="n">constants</span><span class="o">.</span><span class="n">hpo</span><span class="o">.</span><span class="n">base</span><span class="o">.</span><span class="n">PHENOTYPIC_ABNORMALITY</span><span class="p">,</span> <span class="n">term_id</span>
             <span class="p">):</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="s2">&quot;Skipping non phenotype term&quot;</span><span class="p">)</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_NON_PHENOTYPE_TERM</span>
                 <span class="k">continue</span>
 
-            <span class="c1"># get total number of observations</span>
-            <span class="c1"># if term_id not in all_counts:</span>
-            <span class="c1">#     reason_for_filtering_out[&quot;Skipping non-target term&quot;] += 1</span>
-            <span class="c1">#     continue</span>
-
             <span class="n">ph_predicate</span> <span class="o">=</span> <span class="n">ph_predicates</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
             <span class="n">contingency_matrix</span> <span class="o">=</span> <span class="n">counts</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
-            <span class="n">total</span> <span class="o">=</span> <span class="n">contingency_matrix</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
+            
             <span class="n">max_freq</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">get_maximum_group_observed_HPO_frequency</span><span class="p">(</span>
                 <span class="n">contingency_matrix</span><span class="p">,</span>
                 <span class="n">ph_predicate</span><span class="o">=</span><span class="n">ph_predicate</span><span class="p">,</span>
             <span class="p">)</span>
             <span class="k">if</span> <span class="n">max_freq</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hpo_term_frequency_filter</span><span class="p">:</span>
-                <span class="n">reason</span> <span class="o">=</span> <span class="p">(</span>
-                    <span class="s2">&quot;Skipping term with maximum frequency &quot;</span>
-                    <span class="sa">f</span><span class="s2">&quot;that was less than threshold </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_hpo_term_frequency_filter</span><span class="si">}</span><span class="s2">&quot;</span>
-                <span class="p">)</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="n">reason</span><span class="p">)</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_below_frequency_threshold</span>
                 <span class="k">continue</span>
 
-            <span class="k">if</span> <span class="n">contingency_matrix</span><span class="o">.</span><span class="n">shape</span> <span class="o">==</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span> <span class="ow">and</span> <span class="n">total</span> <span class="o">&lt;</span> <span class="mi">7</span><span class="p">:</span>
-                <span class="n">reason</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Skipping term with only </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> observations (not powered for 2x2)&quot;</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="n">reason</span><span class="p">)</span>
+            <span class="n">total_count</span> <span class="o">=</span> <span class="n">contingency_matrix</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">contingency_matrix</span><span class="o">.</span><span class="n">shape</span> <span class="o">==</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span> <span class="ow">and</span> <span class="n">total_count</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">_min_observations_for_2_by_2</span><span class="p">:</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_not_powered_for_2_by_2</span>
+                <span class="k">continue</span>
+            <span class="k">elif</span> <span class="n">contingency_matrix</span><span class="o">.</span><span class="n">shape</span> <span class="o">==</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> <span class="ow">and</span> <span class="n">total_count</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">_min_observations_for_2_by_3</span><span class="p">:</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_not_powered_for_2_by_3</span>
                 <span class="k">continue</span>
 
             <span class="k">if</span> <span class="ow">not</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">some_cell_has_greater_than_one_count</span><span class="p">(</span>
                 <span class="n">counts</span><span class="o">=</span><span class="n">contingency_matrix</span><span class="p">,</span>
                 <span class="n">ph_predicate</span><span class="o">=</span><span class="n">ph_predicate</span><span class="p">,</span>
             <span class="p">):</span>
-                <span class="n">reason</span> <span class="o">=</span> <span class="s2">&quot;Skipping term because no genotype has more than one observed HPO count&quot;</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="n">reason</span><span class="p">)</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO</span>
                 <span class="k">continue</span>
             
             <span class="k">elif</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">genotypes_have_same_hpo_proportions</span><span class="p">(</span>
@@ -469,29 +562,40 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
                 <span class="n">gt_predicate</span><span class="o">=</span><span class="n">gt_predicate</span><span class="p">,</span>
                 <span class="n">ph_predicate</span><span class="o">=</span><span class="n">ph_predicate</span><span class="p">,</span>
             <span class="p">):</span>
-                <span class="n">reason</span> <span class="o">=</span> <span class="s2">&quot;Skipping term because all genotypes have same HPO observed proportions&quot;</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="n">reason</span><span class="p">)</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_SAME_OBSERVED_PROPORTIONS</span>
                 <span class="k">continue</span>
 
             <span class="k">elif</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">one_genotype_has_zero_hpo_observations</span><span class="p">(</span>
                 <span class="n">counts</span><span class="o">=</span><span class="n">contingency_matrix</span><span class="p">,</span>
                 <span class="n">gt_predicate</span><span class="o">=</span><span class="n">gt_predicate</span><span class="p">,</span>
             <span class="p">):</span>
-                <span class="n">reason</span> <span class="o">=</span> <span class="s2">&quot;Skipping term because one genotype had zero observations&quot;</span>
-                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcResult</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="n">reason</span><span class="p">)</span>
+                <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS</span>
                 <span class="k">continue</span>
 
-            <span class="c1"># TODO: the code below actually did not work.</span>
-            <span class="c1"># for child_term_id in self._hpo.graph.get_children(term_id):</span>
-            <span class="c1">#     if child_term_id in tested_counts_pf:</span>
-            <span class="c1">#         if tested_counts_pf[child_term_id].equals(contingency_matrix):</span>
-            <span class="c1">#             # TODO: should we make the match fuzzier by adding a tolerance instead of the exact matches?</span>
-            <span class="c1">#             reason = &quot;Child term with same counts previously tested&quot;</span>
-            <span class="c1">#             reason_for_filtering_out[reason] += 1</span>
-            <span class="c1">#             continue</span>
-
+            <span class="c1"># Check if the term has exactly one child with a very similar number of individuals</span>
+            <span class="c1"># in the genotype and phenotype groups.</span>
+            <span class="n">child_contingency_matrix</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="k">for</span> <span class="n">child</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hpo</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">get_children</span><span class="p">(</span><span class="n">term_id</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">child</span> <span class="ow">in</span> <span class="n">p_to_idx</span><span class="p">:</span>
+                    <span class="n">child_idx</span> <span class="o">=</span> <span class="n">p_to_idx</span><span class="p">[</span><span class="n">child</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">child_contingency_matrix</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                        <span class="n">child_contingency_matrix</span> <span class="o">=</span> <span class="n">counts</span><span class="p">[</span><span class="n">child_idx</span><span class="p">]</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="c1"># Found 2nd child of this term.</span>
+                        <span class="c1"># We always want to test a term with</span>
+                        <span class="c1"># &gt;1 children in the target set.</span>
+                        <span class="n">child_contingency_matrix</span> <span class="o">=</span> <span class="kc">None</span>
+                        <span class="k">break</span>
+            
+            <span class="k">if</span> <span class="n">child_contingency_matrix</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">if</span> <span class="p">(</span><span class="n">contingency_matrix</span> <span class="o">-</span> <span class="n">child_contingency_matrix</span><span class="p">)</span><span class="o">.</span><span class="n">abs</span><span class="p">()</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">:</span>
+                    <span class="c1"># Do not test if the count is exactly the same to the counts in the only child term.</span>
+                    <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SAME_COUNT_AS_THE_ONLY_CHILD</span>
+                    <span class="k">continue</span>
+            
+            <span class="c1"># ##</span>
             <span class="c1"># The term should be tested if we get here.</span>
-            <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ok</span>
+            <span class="n">results</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">PhenotypeMtcFilter</span><span class="o">.</span><span class="n">OK</span>
 
         <span class="c1"># There should be no `None` elements in `results` at this point.</span>
         <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">r</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">results</span><span class="p">):</span>
@@ -508,6 +612,21 @@ <h1>Source code for gpsea.analysis.mtc_filter._impl</h1><div class="highlight"><
         <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">results</span><span class="p">)</span>  <span class="c1"># type: ignore</span></div>
 
 
+<div class="viewcode-block" id="HpoMtcFilter.possible_results">
+<a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.possible_results">[docs]</a>
+    <span class="k">def</span> <span class="nf">possible_results</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Collection</span><span class="p">[</span><span class="n">PhenotypeMtcResult</span><span class="p">]:</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">PhenotypeMtcFilter</span><span class="o">.</span><span class="n">OK</span><span class="p">,</span>
+            <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_GENERAL_TERM</span><span class="p">,</span>
+            <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_NON_PHENOTYPE_TERM</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_below_frequency_threshold</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_not_powered_for_2_by_2</span><span class="p">,</span>
+            <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO</span><span class="p">,</span>
+            <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_SAME_OBSERVED_PROPORTIONS</span><span class="p">,</span>
+            <span class="n">HpoMtcFilter</span><span class="o">.</span><span class="n">SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
 <div class="viewcode-block" id="HpoMtcFilter.filter_method_name">
 <a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.filter_method_name">[docs]</a>
     <span class="k">def</span> <span class="nf">filter_method_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
diff --git a/stable/_modules/gpsea/analysis/pcats/_impl.html b/stable/_modules/gpsea/analysis/pcats/_impl.html
index b0ac5d10b..0544afdb5 100644
--- a/stable/_modules/gpsea/analysis/pcats/_impl.html
+++ b/stable/_modules/gpsea/analysis/pcats/_impl.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pcats._impl &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pcats._impl &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
@@ -96,7 +96,6 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">Patient</span>
 <span class="kn">from</span> <span class="nn">gpsea.analysis.pcats.stats</span> <span class="kn">import</span> <span class="n">CountStatistic</span>
-<span class="kn">from</span> <span class="nn">..predicate</span> <span class="kn">import</span> <span class="n">PatientCategory</span>
 <span class="kn">from</span> <span class="nn">..predicate.genotype</span> <span class="kn">import</span> <span class="n">GenotypePolyPredicate</span>
 <span class="kn">from</span> <span class="nn">..predicate.phenotype</span> <span class="kn">import</span> <span class="n">P</span><span class="p">,</span> <span class="n">PhenotypePolyPredicate</span>
 <span class="kn">from</span> <span class="nn">..mtc_filter</span> <span class="kn">import</span> <span class="n">PhenotypeMtcFilter</span><span class="p">,</span> <span class="n">PhenotypeMtcResult</span>
@@ -189,14 +188,6 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 <span class="sd">    with the order determined by the phenotype order.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="nd">@property</span>
-    <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
-    <span class="k">def</span> <span class="nf">phenotypes</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">P</span><span class="p">]:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Get the tested phenotypes.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">pass</span>
-
     <span class="nd">@property</span>
     <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
     <span class="k">def</span> <span class="nf">n_usable</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">]:</span>
@@ -251,99 +242,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Get total count of tests that were run for this analysis.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span><span class="mi">1</span> <span class="k">for</span> <span class="n">pval</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pvals</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">math</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">pval</span><span class="p">))</span>
-
-<div class="viewcode-block" id="MultiPhenotypeAnalysisResult.summarize">
-<a class="viewcode-back" href="../../../../apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.summarize">[docs]</a>
-    <span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span>
-        <span class="n">hpo</span><span class="p">:</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">MinimalOntology</span><span class="p">,</span>
-        <span class="n">target_phenotype_category</span><span class="p">:</span> <span class="n">PatientCategory</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Create a data frame with summary of the genotype phenotype analysis.</span>
-
-<span class="sd">        The *rows* of the frame correspond to the analyzed HPO terms.</span>
-
-<span class="sd">        The columns of the data frame have `Count` and `Percentage` per used genotype predicate.</span>
-
-<span class="sd">        **Example**</span>
-
-<span class="sd">        If we use :class:`~gpsea.analysis.predicate.genotype.VariantEffectPredicate`</span>
-<span class="sd">        which can compare phenotype with and without a missense variant, we will have a data frame</span>
-<span class="sd">        that looks like this::</span>
-
-<span class="sd">            MISSENSE_VARIANT on `NM_1234.5`                       No                  Yes</span>
-<span class="sd">                                                                  Count    Percent    Count    Percent   Corrected p value  p value</span>
-<span class="sd">            Arachnodactyly [HP:0001166]                           1/10         10%    13/16        81%   0.020299           0.000781</span>
-<span class="sd">            Abnormality of the musculature [HP:0003011]           6/6         100%    11/11       100%   1.000000           1.000000</span>
-<span class="sd">            Abnormal nervous system physiology [HP:0012638]       9/9         100%    15/15       100%   1.000000           1.000000</span>
-<span class="sd">            ...                                                   ...      ...        ...      ...       ...                ...</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-
-        <span class="c1"># TODO: this should be plotted by a formatter.</span>
-        <span class="c1"># Row index: a list of tested HPO terms</span>
-        <span class="n">pheno_idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span>
-        <span class="c1"># Column index: multiindex of counts and percentages for all genotype predicate groups</span>
-        <span class="n">gt_idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_product</span><span class="p">(</span>
-            <span class="c1"># TODO: fix the below</span>
-            <span class="n">iterables</span><span class="o">=</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_gt_predicate</span><span class="o">.</span><span class="n">get_categories</span><span class="p">(),</span> <span class="p">(</span><span class="s2">&quot;Count&quot;</span><span class="p">,</span> <span class="s2">&quot;Percent&quot;</span><span class="p">)),</span>
-            <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_gt_predicate</span><span class="o">.</span><span class="n">get_question_base</span><span class="p">(),</span> <span class="kc">None</span><span class="p">),</span>
-        <span class="p">)</span>
-
-        <span class="c1"># We&#39;ll fill this frame with data</span>
-        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">index</span><span class="o">=</span><span class="n">pheno_idx</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="n">gt_idx</span><span class="p">)</span>
-
-        <span class="k">for</span> <span class="n">phenotype</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">all_counts</span><span class="p">):</span>
-            <span class="n">gt_totals</span> <span class="o">=</span> <span class="p">(</span>
-                <span class="n">count</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
-            <span class="p">)</span>  <span class="c1"># Sum across the phenotype categories (collapse the rows).</span>
-            <span class="k">for</span> <span class="n">gt_cat</span> <span class="ow">in</span> <span class="n">count</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
-                <span class="n">cnt</span> <span class="o">=</span> <span class="n">count</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">target_phenotype_category</span><span class="p">,</span> <span class="n">gt_cat</span><span class="p">]</span>
-                <span class="n">total</span> <span class="o">=</span> <span class="n">gt_totals</span><span class="p">[</span><span class="n">gt_cat</span><span class="p">]</span>
-                <span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">phenotype</span><span class="p">,</span> <span class="p">(</span><span class="n">gt_cat</span><span class="p">,</span> <span class="s2">&quot;Count&quot;</span><span class="p">)]</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">cnt</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">&quot;</span>
-                <span class="n">pct</span> <span class="o">=</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">total</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="nb">round</span><span class="p">(</span><span class="n">cnt</span> <span class="o">*</span> <span class="mi">100</span> <span class="o">/</span> <span class="n">total</span><span class="p">)</span>
-                <span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">phenotype</span><span class="p">,</span> <span class="p">(</span><span class="n">gt_cat</span><span class="p">,</span> <span class="s2">&quot;Percent&quot;</span><span class="p">)]</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">pct</span><span class="si">}</span><span class="s2">%&quot;</span>
-
-        <span class="c1"># Add columns with p values and corrected p values (if present)</span>
-        <span class="n">p_val_col_name</span> <span class="o">=</span> <span class="s2">&quot;p values&quot;</span>
-        <span class="n">corrected_p_val_col_name</span> <span class="o">=</span> <span class="s2">&quot;Corrected p values&quot;</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">corrected_pvals</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="n">df</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span>
-                <span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">corrected_p_val_col_name</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">corrected_pvals</span>
-            <span class="p">)</span>
-        <span class="n">df</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">pvals</span><span class="p">)</span>
-
-        <span class="c1"># Format the index values: `HP:0001250` -&gt; `Seizure [HP:0001250]` if the index members are HPO terms</span>
-        <span class="c1"># or just use the term ID CURIE otherwise (e.g. `OMIM:123000`).</span>
-        <span class="n">labeled_idx</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">map</span><span class="p">(</span>
-            <span class="k">lambda</span> <span class="n">term_id</span><span class="p">:</span> <span class="n">MultiPhenotypeAnalysisResult</span><span class="o">.</span><span class="n">_format_term_id</span><span class="p">(</span><span class="n">hpo</span><span class="p">,</span> <span class="n">term_id</span><span class="p">)</span>
-        <span class="p">)</span>
-
-        <span class="c1"># Last, sort by corrected p value or just p value</span>
-        <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="n">labeled_idx</span><span class="p">)</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">corrected_pvals</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span>
-                <span class="n">by</span><span class="o">=</span><span class="p">[(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">corrected_p_val_col_name</span><span class="p">),</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">)]</span>
-            <span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">))</span></div>
-
-
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">_format_term_id</span><span class="p">(</span>
-        <span class="n">hpo</span><span class="p">:</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">MinimalOntology</span><span class="p">,</span>
-        <span class="n">term_id</span><span class="p">:</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Format a `term_id` as a `str`. HPO term ID is formatted as `&lt;name&gt; [&lt;term_id&gt;]` whereas other term IDs</span>
-<span class="sd">        are formatted as CURIEs (e.g. `OMIM:123000`).</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">if</span> <span class="n">term_id</span><span class="o">.</span><span class="n">prefix</span> <span class="o">==</span> <span class="s2">&quot;HP&quot;</span><span class="p">:</span>
-            <span class="n">term_name</span> <span class="o">=</span> <span class="n">hpo</span><span class="o">.</span><span class="n">get_term_name</span><span class="p">(</span><span class="n">term_id</span><span class="p">)</span>
-            <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">term_name</span><span class="si">}</span><span class="s2"> [</span><span class="si">{</span><span class="n">term_id</span><span class="o">.</span><span class="n">value</span><span class="si">}</span><span class="s2">]&quot;</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">term_id</span><span class="o">.</span><span class="n">value</span></div>
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span><span class="mi">1</span> <span class="k">for</span> <span class="n">pval</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pvals</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">math</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">pval</span><span class="p">))</span></div>
 
 
 
@@ -474,7 +373,8 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">_apply_mtc</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">pvals</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">float</span><span class="p">],</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">float</span><span class="p">]]:</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">float</span><span class="p">]:</span>
+        <span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mtc_correction</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
         <span class="n">_</span><span class="p">,</span> <span class="n">corrected_pvals</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">multitest</span><span class="o">.</span><span class="n">multipletests</span><span class="p">(</span>
             <span class="n">pvals</span><span class="o">=</span><span class="n">pvals</span><span class="p">,</span>
             <span class="n">alpha</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_mtc_alpha</span><span class="p">,</span>
@@ -490,14 +390,14 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
-        <span class="n">phenotypes</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">P</span><span class="p">],</span>
+        <span class="n">pheno_predicates</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Iterable</span><span class="p">[</span><span class="n">PhenotypePolyPredicate</span><span class="p">[</span><span class="n">P</span><span class="p">]],</span>
         <span class="n">n_usable</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span>
         <span class="n">all_counts</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">],</span>
         <span class="n">pvals</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">float</span><span class="p">],</span>
         <span class="n">corrected_pvals</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">float</span><span class="p">]],</span>
         <span class="n">gt_predicate</span><span class="p">:</span> <span class="n">GenotypePolyPredicate</span><span class="p">,</span>
     <span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_phenotypes</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">phenotypes</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_pheno_predicates</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">pheno_predicates</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_n_usable</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">n_usable</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_all_counts</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">all_counts</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_pvals</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">pvals</span><span class="p">)</span>
@@ -507,9 +407,19 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
         <span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">gt_predicate</span><span class="p">,</span> <span class="n">GenotypePolyPredicate</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_gt_predicate</span> <span class="o">=</span> <span class="n">gt_predicate</span>
 
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">gt_predicate</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gt_predicate</span>
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">pheno_predicates</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">PhenotypePolyPredicate</span><span class="p">[</span><span class="n">P</span><span class="p">]]:</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pheno_predicates</span>
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">phenotypes</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">P</span><span class="p">]:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phenotypes</span>
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">phenotype</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pheno_predicates</span><span class="p">)</span>
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">n_usable</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">]:</span>
@@ -529,7 +439,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
         <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">BaseMultiPhenotypeAnalysisResult</span><span class="p">)</span> \
-            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phenotypes</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_phenotypes</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pheno_predicates</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_pheno_predicates</span> \
             <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_usable</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_n_usable</span> \
             <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_all_counts</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_all_counts</span> \
             <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pvals</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_pvals</span> \
@@ -539,7 +449,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="c1"># NOTE: if a field is added, the hash method of the subclasses must be updated as well.</span>
         <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_phenotypes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_usable</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_all_counts</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_pheno_predicates</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_usable</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_all_counts</span><span class="p">,</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_pvals</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_corrected_pvals</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gt_predicate</span><span class="p">,</span>
         <span class="p">))</span>
 
@@ -574,10 +484,8 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">corrected_pvals</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_apply_mtc</span><span class="p">(</span><span class="n">pvals</span><span class="o">=</span><span class="n">pvals</span><span class="p">)</span>
 
-        <span class="n">phenotypes</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">phenotype</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pheno_predicates</span><span class="p">)</span>
-
         <span class="k">return</span> <span class="n">BaseMultiPhenotypeAnalysisResult</span><span class="p">(</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="n">phenotypes</span><span class="p">,</span>
+            <span class="n">pheno_predicates</span><span class="o">=</span><span class="n">pheno_predicates</span><span class="p">,</span>
             <span class="n">n_usable</span><span class="o">=</span><span class="n">n_usable</span><span class="p">,</span>
             <span class="n">all_counts</span><span class="o">=</span><span class="n">all_counts</span><span class="p">,</span>
             <span class="n">pvals</span><span class="o">=</span><span class="n">pvals</span><span class="p">,</span>
@@ -599,7 +507,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
-        <span class="n">phenotypes</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">],</span>
+        <span class="n">pheno_predicates</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Iterable</span><span class="p">[</span><span class="n">PhenotypePolyPredicate</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">]],</span>
         <span class="n">n_usable</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span>
         <span class="n">all_counts</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">],</span>
         <span class="n">pvals</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">float</span><span class="p">],</span>
@@ -610,7 +518,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
         <span class="n">mtc_name</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
     <span class="p">):</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="n">phenotypes</span><span class="p">,</span>
+            <span class="n">pheno_predicates</span><span class="o">=</span><span class="n">pheno_predicates</span><span class="p">,</span>
             <span class="n">n_usable</span><span class="o">=</span><span class="n">n_usable</span><span class="p">,</span>
             <span class="n">all_counts</span><span class="o">=</span><span class="n">all_counts</span><span class="p">,</span>
             <span class="n">pvals</span><span class="o">=</span><span class="n">pvals</span><span class="p">,</span>
@@ -652,7 +560,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_phenotypes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_usable</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_all_counts</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_pheno_predicates</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_n_usable</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_all_counts</span><span class="p">,</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_pvals</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_corrected_pvals</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gt_predicate</span><span class="p">,</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_mtc_filter_name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mtc_filter_results</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mtc_name</span><span class="p">,</span>
         <span class="p">))</span></div>
@@ -696,7 +604,6 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
         <span class="n">pheno_predicates</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">pheno_predicates</span><span class="p">)</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pheno_predicates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No phenotype predicates were provided&quot;</span><span class="p">)</span>
-        <span class="n">phenotypes</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">phenotype</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pheno_predicates</span><span class="p">)</span>
 
         <span class="c1"># 1 - Count the patients</span>
         <span class="n">n_usable</span><span class="p">,</span> <span class="n">all_counts</span> <span class="o">=</span> <span class="n">apply_predicates_on_patients</span><span class="p">(</span>
@@ -731,7 +638,7 @@ <h1>Source code for gpsea.analysis.pcats._impl</h1><div class="highlight"><pre>
             <span class="n">corrected_pvals</span><span class="p">[</span><span class="n">mtc_mask</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_apply_mtc</span><span class="p">(</span><span class="n">pvals</span><span class="o">=</span><span class="n">pvals</span><span class="p">[</span><span class="n">mtc_mask</span><span class="p">])</span>
 
         <span class="k">return</span> <span class="n">HpoTermAnalysisResult</span><span class="p">(</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="n">phenotypes</span><span class="p">,</span>
+            <span class="n">pheno_predicates</span><span class="o">=</span><span class="n">pheno_predicates</span><span class="p">,</span>
             <span class="n">n_usable</span><span class="o">=</span><span class="n">n_usable</span><span class="p">,</span>
             <span class="n">all_counts</span><span class="o">=</span><span class="n">all_counts</span><span class="p">,</span>
             <span class="n">pvals</span><span class="o">=</span><span class="n">pvals</span><span class="p">,</span>
diff --git a/stable/_modules/gpsea/analysis/pcats/stats/_stats.html b/stable/_modules/gpsea/analysis/pcats/stats/_stats.html
index 6fc93c82c..c8e1086ca 100644
--- a/stable/_modules/gpsea/analysis/pcats/stats/_stats.html
+++ b/stable/_modules/gpsea/analysis/pcats/stats/_stats.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pcats.stats._stats &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pcats.stats._stats &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/analysis/predicate/_api.html b/stable/_modules/gpsea/analysis/predicate/_api.html
index a25353f6b..27a30ffe5 100644
--- a/stable/_modules/gpsea/analysis/predicate/_api.html
+++ b/stable/_modules/gpsea/analysis/predicate/_api.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate._api &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate._api &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/analysis/predicate/genotype/_api.html b/stable/_modules/gpsea/analysis/predicate/genotype/_api.html
index 79d8c8491..93086732f 100644
--- a/stable/_modules/gpsea/analysis/predicate/genotype/_api.html
+++ b/stable/_modules/gpsea/analysis/predicate/genotype/_api.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.genotype._api &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.genotype._api &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/analysis/predicate/genotype/_counter.html b/stable/_modules/gpsea/analysis/predicate/genotype/_counter.html
index 562c8e959..8bfd89446 100644
--- a/stable/_modules/gpsea/analysis/predicate/genotype/_counter.html
+++ b/stable/_modules/gpsea/analysis/predicate/genotype/_counter.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.genotype._counter &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.genotype._counter &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
@@ -93,13 +93,14 @@ <h1>Source code for gpsea.analysis.predicate.genotype._counter</h1><div class="h
 
 <span class="sd">    :param predicate: a :class:`VariantPredicate` for selecting the target variants.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># TODO: this class should probably be an implementation detail, </span>
+    <span class="c1"># TODO: this class should probably be an implementation detail,</span>
     <span class="c1">#   and not a public member of the package.</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
     <span class="p">):</span>
+        <span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">predicate</span><span class="p">,</span> <span class="n">VariantPredicate</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_predicate</span> <span class="o">=</span> <span class="n">predicate</span>
 
 <div class="viewcode-block" id="AlleleCounter.get_question">
diff --git a/stable/_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html b/stable/_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html
index b3a59e914..e28f5a5c3 100644
--- a/stable/_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html
+++ b/stable/_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.genotype._gt_predicates &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.genotype._gt_predicates &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
@@ -81,10 +81,9 @@
            <div itemprop="articleBody">
              
   <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">cProfile</span> <span class="kn">import</span> <span class="n">label</span>
-<span class="kn">import</span> <span class="nn">dataclasses</span>
-<span class="kn">import</span> <span class="nn">enum</span>
+<span></span><span class="kn">import</span> <span class="nn">dataclasses</span>
 <span class="kn">import</span> <span class="nn">typing</span>
+<span class="kn">import</span> <span class="nn">warnings</span>
 
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">defaultdict</span>
 
@@ -92,82 +91,11 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
 
 <span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">Patient</span><span class="p">,</span> <span class="n">Sex</span>
 
-<span class="kn">from</span> <span class="nn">.._api</span> <span class="kn">import</span> <span class="n">Categorization</span><span class="p">,</span> <span class="n">PatientCategory</span><span class="p">,</span> <span class="n">PatientCategories</span>
+<span class="kn">from</span> <span class="nn">.._api</span> <span class="kn">import</span> <span class="n">Categorization</span><span class="p">,</span> <span class="n">PatientCategory</span>
 <span class="kn">from</span> <span class="nn">._api</span> <span class="kn">import</span> <span class="n">GenotypePolyPredicate</span>
 <span class="kn">from</span> <span class="nn">._api</span> <span class="kn">import</span> <span class="n">VariantPredicate</span>
 <span class="kn">from</span> <span class="nn">._counter</span> <span class="kn">import</span> <span class="n">AlleleCounter</span>
-
-
-<span class="k">class</span> <span class="nc">AlleleCountingGenotypeBooleanPredicate</span><span class="p">(</span><span class="n">GenotypePolyPredicate</span><span class="p">):</span>
-    <span class="c1"># NOT PART OF THE PUBLIC API</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    The predicate tests presence of at least one matching allele in the patient.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">YES</span> <span class="o">=</span> <span class="n">Categorization</span><span class="p">(</span><span class="n">PatientCategories</span><span class="o">.</span><span class="n">YES</span><span class="p">)</span>
-    <span class="n">NO</span> <span class="o">=</span> <span class="n">Categorization</span><span class="p">(</span><span class="n">PatientCategories</span><span class="o">.</span><span class="n">NO</span><span class="p">)</span>
-
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">for_variant_predicate</span><span class="p">(</span><span class="n">predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">):</span>
-        <span class="n">allele_counter</span> <span class="o">=</span> <span class="n">AlleleCounter</span><span class="p">(</span><span class="n">predicate</span><span class="o">=</span><span class="n">predicate</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="p">(</span><span class="n">allele_counter</span><span class="o">=</span><span class="n">allele_counter</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">allele_counter</span><span class="p">:</span> <span class="n">AlleleCounter</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span> <span class="o">=</span> <span class="n">allele_counter</span>
-
-    <span class="k">def</span> <span class="nf">get_categorizations</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        The predicate bins a patient into</span>
-<span class="sd">        :attr:`AlleleCountingGenotypeBooleanPredicate.NO`</span>
-<span class="sd">        or :class:`AlleleCountingGenotypeBooleanPredicate.YES` category.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="p">(</span>
-            <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="o">.</span><span class="n">YES</span><span class="p">,</span>
-            <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="o">.</span><span class="n">NO</span><span class="p">,</span>
-        <span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_question_base</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
-
-    <span class="k">def</span> <span class="nf">test</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">patient</span><span class="p">:</span> <span class="n">Patient</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_check_patient</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
-
-        <span class="n">allele_count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
-        <span class="k">if</span> <span class="n">allele_count</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="o">.</span><span class="n">YES</span>
-        <span class="k">elif</span> <span class="n">allele_count</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="o">.</span><span class="n">NO</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;Allele counter should return a non-negative allele count: </span><span class="si">{</span><span class="n">allele_count</span><span class="si">}</span><span class="s2">&quot;</span>
-            <span class="p">)</span>
-
-    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-        <span class="k">return</span> <span class="p">(</span>
-            <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="p">)</span>
-            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_allele_counter</span>
-        <span class="p">)</span>
-
-    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
-        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="p">,))</span>
-
-    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;AlleleCountingGenotypeBooleanPredicate(allele_counter=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="si">}</span><span class="s2">)&quot;</span>
-
-    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
-
-
-<div class="viewcode-block" id="boolean_predicate">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.boolean_predicate">[docs]</a>
-<span class="k">def</span> <span class="nf">boolean_predicate</span><span class="p">(</span><span class="n">variant_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Create a genotype boolean predicate from given `variant_predicate`</span>
-<span class="sd">    to test for presence of at least one matching allele in the patient.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">AlleleCountingGenotypeBooleanPredicate</span><span class="o">.</span><span class="n">for_variant_predicate</span><span class="p">(</span>
-        <span class="n">predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
-    <span class="p">)</span></div>
-
+<span class="kn">from</span> <span class="nn">._variant</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
 
 
 <span class="k">class</span> <span class="nc">AlleleCountingGroupsPredicate</span><span class="p">(</span><span class="n">GenotypePolyPredicate</span><span class="p">):</span>
@@ -275,128 +203,259 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
 
 
 
-<span class="k">class</span> <span class="nc">FilteringGenotypePolyPredicate</span><span class="p">(</span><span class="n">GenotypePolyPredicate</span><span class="p">):</span>
-    <span class="c1"># NOT PART OF THE PUBLIC API</span>
+<span class="k">class</span> <span class="nc">PolyCountingGenotypePredicate</span><span class="p">(</span><span class="n">GenotypePolyPredicate</span><span class="p">):</span>
 
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">create</span><span class="p">(</span>
-        <span class="n">predicate</span><span class="p">:</span> <span class="s2">&quot;GenotypePolyPredicate&quot;</span><span class="p">,</span>
-        <span class="n">targets</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Collection</span><span class="p">[</span><span class="n">Categorization</span><span class="p">],</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;FilteringGenotypePolyPredicate&quot;</span><span class="p">:</span>
-        <span class="c1"># At least 2 target categorizations must be provided</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">targets</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">1</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;At least 2 target categorizations must be provided but got </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">targets</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span>
-            <span class="p">)</span>
-
-        <span class="n">good_boys</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">cat</span><span class="p">,</span> <span class="n">Categorization</span><span class="p">)</span> <span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="n">targets</span><span class="p">)</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">good_boys</span><span class="p">):</span>
-            <span class="n">offenders</span> <span class="o">=</span> <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
-                <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">is_instance</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">good_boys</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">is_instance</span>
-            <span class="p">)</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;The targets at following indices are not categorizations: [</span><span class="si">{</span><span class="n">offenders</span><span class="si">}</span><span class="s2">]&quot;</span>
-            <span class="p">)</span>
+    <span class="k">def</span> <span class="nf">monoallelic</span><span class="p">(</span>
+        <span class="n">a_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+        <span class="n">b_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+        <span class="n">names</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">],</span>
+    <span class="p">):</span>
+        <span class="n">count2cat</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">):</span> <span class="n">Categorization</span><span class="p">(</span><span class="n">PatientCategory</span><span class="p">(</span><span class="n">cat_id</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Monoallelic </span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)),</span>
+            <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">):</span> <span class="n">Categorization</span><span class="p">(</span><span class="n">PatientCategory</span><span class="p">(</span><span class="n">cat_id</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Monoallelic </span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)),</span>
+        <span class="p">}</span>
 
-        <span class="c1"># All `allowed` categorizations must in fact be present in the `base` predicate.</span>
-        <span class="n">cats_are_in_fact_present</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
-            <span class="n">cat</span> <span class="ow">in</span> <span class="n">predicate</span><span class="o">.</span><span class="n">get_categorizations</span><span class="p">()</span> <span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="n">targets</span>
+        <span class="k">return</span> <span class="n">PolyCountingGenotypePredicate</span><span class="o">.</span><span class="n">_for_predicates_and_categories</span><span class="p">(</span>
+            <span class="n">count2cat</span><span class="o">=</span><span class="n">count2cat</span><span class="p">,</span>
+            <span class="n">a_predicate</span><span class="o">=</span><span class="n">a_predicate</span><span class="p">,</span>
+            <span class="n">b_predicate</span><span class="o">=</span><span class="n">b_predicate</span><span class="p">,</span>
         <span class="p">)</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">cats_are_in_fact_present</span><span class="p">):</span>
-            <span class="n">missing</span> <span class="o">=</span> <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
-                <span class="n">c</span><span class="o">.</span><span class="n">category</span><span class="o">.</span><span class="n">name</span>
-                <span class="k">for</span> <span class="n">c</span><span class="p">,</span> <span class="n">is_present</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">targets</span><span class="p">,</span> <span class="n">cats_are_in_fact_present</span><span class="p">)</span>
-                <span class="k">if</span> <span class="ow">not</span> <span class="n">is_present</span>
-            <span class="p">)</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Some from the categories are not present: </span><span class="si">{</span><span class="n">missing</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">targets</span><span class="p">)</span> <span class="o">==</span> <span class="n">predicate</span><span class="o">.</span><span class="n">n_categorizations</span><span class="p">():</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;It makes no sense to subset the a predicate with </span><span class="si">{</span><span class="n">predicate</span><span class="o">.</span><span class="n">n_categorizations</span><span class="p">()</span><span class="si">}</span><span class="s2"> categorizations &quot;</span>
-                <span class="sa">f</span><span class="s2">&quot;with the same number (</span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">targets</span><span class="p">)</span><span class="si">}</span><span class="s2">) of targets&quot;</span>
-            <span class="p">)</span>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">biallelic</span><span class="p">(</span>
+        <span class="n">a_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+        <span class="n">b_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+        <span class="n">names</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">],</span>
+    <span class="p">):</span>
+        <span class="n">count2cat</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">):</span> <span class="n">Categorization</span><span class="p">(</span>
+                <span class="n">PatientCategory</span><span class="p">(</span>
+                    <span class="n">cat_id</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Biallelic </span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">),</span>
+            <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">):</span> <span class="n">Categorization</span><span class="p">(</span>
+                <span class="n">PatientCategory</span><span class="p">(</span>
+                    <span class="n">cat_id</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
+                <span class="p">),</span>
+            <span class="p">),</span>
+            <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">):</span> <span class="n">Categorization</span><span class="p">(</span>
+                <span class="n">PatientCategory</span><span class="p">(</span>
+                    <span class="n">cat_id</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Biallelic </span><span class="si">{</span><span class="n">names</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span>
+                <span class="p">),</span>
+            <span class="p">),</span>
+        <span class="p">}</span>
 
-        <span class="k">return</span> <span class="n">FilteringGenotypePolyPredicate</span><span class="p">(</span>
-            <span class="n">predicate</span><span class="o">=</span><span class="n">predicate</span><span class="p">,</span>
-            <span class="n">allowed</span><span class="o">=</span><span class="n">targets</span><span class="p">,</span>
+        <span class="k">return</span> <span class="n">PolyCountingGenotypePredicate</span><span class="o">.</span><span class="n">_for_predicates_and_categories</span><span class="p">(</span>
+            <span class="n">count2cat</span><span class="o">=</span><span class="n">count2cat</span><span class="p">,</span>
+            <span class="n">a_predicate</span><span class="o">=</span><span class="n">a_predicate</span><span class="p">,</span>
+            <span class="n">b_predicate</span><span class="o">=</span><span class="n">b_predicate</span><span class="p">,</span>
+        <span class="p">)</span>
+    
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_for_predicates_and_categories</span><span class="p">(</span>
+        <span class="n">count2cat</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Mapping</span><span class="p">[</span><span class="n">typing</span><span class="o">.</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">],</span> <span class="n">Categorization</span><span class="p">],</span>
+        <span class="n">a_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+        <span class="n">b_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;PolyCountingGenotypePredicate&quot;</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">PolyCountingGenotypePredicate</span><span class="p">(</span>
+            <span class="n">a_counter</span><span class="o">=</span><span class="n">AlleleCounter</span><span class="p">(</span><span class="n">a_predicate</span><span class="p">),</span>
+            <span class="n">b_counter</span><span class="o">=</span><span class="n">AlleleCounter</span><span class="p">(</span><span class="n">b_predicate</span><span class="p">),</span>
+            <span class="n">count2cat</span><span class="o">=</span><span class="n">count2cat</span><span class="p">,</span>
         <span class="p">)</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
-        <span class="n">predicate</span><span class="p">:</span> <span class="s2">&quot;GenotypePolyPredicate&quot;</span><span class="p">,</span>
-        <span class="n">allowed</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Iterable</span><span class="p">[</span><span class="n">Categorization</span><span class="p">],</span>
+        <span class="n">count2cat</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Mapping</span><span class="p">[</span><span class="n">typing</span><span class="o">.</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">],</span> <span class="n">Categorization</span><span class="p">],</span>
+        <span class="n">a_counter</span><span class="p">:</span> <span class="n">AlleleCounter</span><span class="p">,</span>
+        <span class="n">b_counter</span><span class="p">:</span> <span class="n">AlleleCounter</span><span class="p">,</span>
     <span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_predicate</span> <span class="o">=</span> <span class="n">predicate</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_allowed</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">allowed</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_count2cat</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">count2cat</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_categorizations</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">count2cat</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_a_counter</span> <span class="o">=</span> <span class="n">a_counter</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_b_counter</span> <span class="o">=</span> <span class="n">b_counter</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_hash</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_hash</span><span class="p">()</span>
+    
+    <span class="k">def</span> <span class="nf">_compute_hash</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+        <span class="n">hash_value</span> <span class="o">=</span> <span class="mi">17</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_groups</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">count</span><span class="p">,</span> <span class="n">cat</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_count2cat</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="n">hash_value</span> <span class="o">+=</span> <span class="mi">13</span> <span class="o">*</span> <span class="nb">hash</span><span class="p">(</span><span class="n">count</span><span class="p">)</span>
+            <span class="n">hash_value</span> <span class="o">+=</span> <span class="mi">13</span> <span class="o">*</span> <span class="nb">hash</span><span class="p">(</span><span class="n">cat</span><span class="p">)</span>
+
+        <span class="n">hash_value</span> <span class="o">+=</span> <span class="mi">23</span> <span class="o">*</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_a_counter</span><span class="p">)</span>
+        <span class="n">hash_value</span> <span class="o">+=</span> <span class="mi">23</span> <span class="o">*</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_b_counter</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">hash_value</span>
 
     <span class="k">def</span> <span class="nf">get_categorizations</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allowed</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_categorizations</span>
 
     <span class="k">def</span> <span class="nf">get_question_base</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_predicate</span><span class="o">.</span><span class="n">get_question_base</span><span class="p">()</span>
+        <span class="k">return</span> <span class="s1">&#39;Allele group&#39;</span>
 
     <span class="k">def</span> <span class="nf">test</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">patient</span><span class="p">:</span> <span class="n">Patient</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
-        <span class="n">cat</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_predicate</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
-        <span class="k">if</span> <span class="n">cat</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allowed</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">cat</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_check_patient</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
+
+        <span class="n">a_count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_a_counter</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
+        <span class="n">b_count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_b_counter</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
+        <span class="n">counts</span> <span class="o">=</span> <span class="p">(</span><span class="n">a_count</span><span class="p">,</span> <span class="n">b_count</span><span class="p">)</span>
+        
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_count2cat</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">counts</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
 
-    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;FilteringGenotypePolyPredicate(predicate=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_predicate</span><span class="si">}</span><span class="s2">, allowed=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_allowed</span><span class="si">}</span><span class="s2">)&quot;</span>
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">PolyCountingGenotypePredicate</span><span class="p">)</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_count2cat</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_count2cat</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_a_counter</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_a_counter</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_b_counter</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_b_counter</span>
+    
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hash</span>
 
 
-<div class="viewcode-block" id="filtering_predicate">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.filtering_predicate">[docs]</a>
-<span class="k">def</span> <span class="nf">filtering_predicate</span><span class="p">(</span>
-    <span class="n">predicate</span><span class="p">:</span> <span class="n">GenotypePolyPredicate</span><span class="p">,</span>
-    <span class="n">targets</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Collection</span><span class="p">[</span><span class="n">Categorization</span><span class="p">],</span>
+<div class="viewcode-block" id="monoallelic_predicate">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.monoallelic_predicate">[docs]</a>
+<span class="k">def</span> <span class="nf">monoallelic_predicate</span><span class="p">(</span>
+    <span class="n">a_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+    <span class="n">b_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+    <span class="n">names</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">),</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Filtering predicate applies the base `predicate` but only returns the categorizations</span>
-<span class="sd">    from the provided `targets` collection.</span>
-
-<span class="sd">    This can be useful if only some of the categorizations are interesting.</span>
-<span class="sd">    For instance, if we only seek to compare the differences between heterozygous and hemizygous variants,</span>
-<span class="sd">    but the predicate also bins the patients into homozygous reference, and biallelic alt genotype groups.</span>
+<span class="sd">    The predicate bins patient into one of two groups, `A` and `B`,</span>
+<span class="sd">    based on presence of *exactly* one allele of a variant</span>
+<span class="sd">    that meets the predicate criteria.</span>
+
+<span class="sd">    The number of alleles :math:`count_{A}` and :math:`count_{B}`</span>
+<span class="sd">    is computed using `a_predicate` and `b_predicate`</span>
+<span class="sd">    and the individual is assigned into a group</span>
+<span class="sd">    based on the following table:</span>
+<span class="sd">    </span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+<span class="sd">    | Group     | :math:`count_{A}` | :math:`count_{B}` |</span>
+<span class="sd">    +===========+===================+===================+</span>
+<span class="sd">    | A         | 1                 | 0                 |</span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+<span class="sd">    | B         | 0                 | 1                 |</span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+
+<span class="sd">    The individuals with different allele counts</span>
+<span class="sd">    (e.g. :math:`count_{A} = 0` and :math:`count_{B} = 2`)</span>
+<span class="sd">    are assigned into the ``None`` group and, thus, omitted from the analysis.</span>
+
+<span class="sd">    :param a_predicate: predicate to test if the variants</span>
+<span class="sd">        meet the criteria of the first group (named `A` by default).</span>
+<span class="sd">    :param b_predicate: predicate to test if the variants</span>
+<span class="sd">        meet the criteria of the second group (named `B` by default).</span>
+<span class="sd">    :param names: group names (default ``(&#39;A&#39;, &#39;B&#39;)``).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">PolyCountingGenotypePredicate</span><span class="o">.</span><span class="n">monoallelic</span><span class="p">(</span>
+        <span class="n">a_predicate</span><span class="o">=</span><span class="n">a_predicate</span><span class="p">,</span>
+        <span class="n">b_predicate</span><span class="o">=</span><span class="n">b_predicate</span><span class="p">,</span>
+        <span class="n">names</span><span class="o">=</span><span class="n">names</span><span class="p">,</span>
+    <span class="p">)</span></div>
 
-<span class="sd">    See the :ref:`filtering-predicate` section for an example.</span>
 
-<span class="sd">    The `predicate` is checked for being able to produce the all items in `targets`</span>
-<span class="sd">    and the `targets` must include at least 2 categorizations.</span>
 
-<span class="sd">    :param predicate: the base predicate whose categorizations are subject to filteration.</span>
-<span class="sd">    :param targets: the categorizations to retain</span>
+<div class="viewcode-block" id="biallelic_predicate">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.biallelic_predicate">[docs]</a>
+<span class="k">def</span> <span class="nf">biallelic_predicate</span><span class="p">(</span>
+    <span class="n">a_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+    <span class="n">b_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
+    <span class="n">names</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">),</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    The predicate bins patient into one of the three groups,</span>
+<span class="sd">    `AA`, `AB`, and `BB`,</span>
+<span class="sd">    based on presence of one or two variant alleles</span>
+<span class="sd">    that meet the predicate criteria.</span>
+
+<span class="sd">    The number of alleles :math:`count_{A}` and :math:`count_{B}`</span>
+<span class="sd">    is computed using `a_predicate` and `b_predicate`</span>
+<span class="sd">    and the individual is assigned into a group</span>
+<span class="sd">    based on the following table:</span>
+<span class="sd">    </span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+<span class="sd">    | Group     | :math:`count_{A}` | :math:`count_{B}` |</span>
+<span class="sd">    +===========+===================+===================+</span>
+<span class="sd">    | AA        | 2                 | 0                 |</span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+<span class="sd">    | AB        | 1                 | 1                 |</span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+<span class="sd">    | AA        | 0                 | 2                 |</span>
+<span class="sd">    +-----------+-------------------+-------------------+</span>
+
+<span class="sd">    The individuals with different allele counts</span>
+<span class="sd">    (e.g. :math:`count_{A} = 1` and :math:`count_{B} = 2`)</span>
+<span class="sd">    are assigned into the ``None`` group and will be, thus,</span>
+<span class="sd">    omitted from the analysis.</span>
+
+<span class="sd">    :param a_predicate: predicate to test if the variants</span>
+<span class="sd">        meet the criteria of the first group (named `A` by default).</span>
+<span class="sd">    :param b_predicate: predicate to test if the variants</span>
+<span class="sd">        meet the criteria of the second group (named `B` by default).</span>
+<span class="sd">    :param names: group names (default ``(&#39;A&#39;, &#39;B&#39;)``).</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">FilteringGenotypePolyPredicate</span><span class="o">.</span><span class="n">create</span><span class="p">(</span>
-        <span class="n">predicate</span><span class="o">=</span><span class="n">predicate</span><span class="p">,</span>
-        <span class="n">targets</span><span class="o">=</span><span class="n">targets</span><span class="p">,</span>
+    <span class="k">return</span> <span class="n">PolyCountingGenotypePredicate</span><span class="o">.</span><span class="n">biallelic</span><span class="p">(</span>
+        <span class="n">a_predicate</span><span class="o">=</span><span class="n">a_predicate</span><span class="p">,</span>
+        <span class="n">b_predicate</span><span class="o">=</span><span class="n">b_predicate</span><span class="p">,</span>
+        <span class="n">names</span><span class="o">=</span><span class="n">names</span><span class="p">,</span>
     <span class="p">)</span></div>
 
 
 
-<span class="nd">@dataclasses</span><span class="o">.</span><span class="n">dataclass</span><span class="p">(</span><span class="n">eq</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">frozen</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-<span class="k">class</span> <span class="nc">GenotypeGroup</span><span class="p">:</span>
-    <span class="n">allele_count</span><span class="p">:</span> <span class="nb">int</span>
-    <span class="n">sex</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">Sex</span><span class="p">]</span>
-    <span class="n">categorization</span><span class="p">:</span> <span class="n">Categorization</span>
-
-
-<span class="k">class</span> <span class="nc">MendelianInheritanceAspect</span><span class="p">(</span><span class="n">enum</span><span class="o">.</span><span class="n">Enum</span><span class="p">):</span>
-    <span class="n">AUTOSOMAL</span> <span class="o">=</span> <span class="mi">0</span>
+<div class="viewcode-block" id="autosomal_dominant">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_dominant">[docs]</a>
+<span class="k">def</span> <span class="nf">autosomal_dominant</span><span class="p">(</span>
+    <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">VariantPredicate</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Related to chromosomes that do *not* determine the sex of an individual.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
+<span class="sd">    Create a predicate that assigns the patient either</span>
+<span class="sd">    into homozygous reference or heterozygous</span>
+<span class="sd">    group in line with the autosomal dominant mode of inheritance.</span>
 
-    <span class="n">GONOSOMAL</span> <span class="o">=</span> <span class="mi">1</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Related to chromosomes that determine the sex of an individual.</span>
+<span class="sd">    :param variant_predicate: a predicate for choosing the variants for testing</span>
+<span class="sd">        or `None` if all variants should be used.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">variant_predicate</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">variant_predicate</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">true</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">_from_moi_info</span><span class="p">(</span>
+        <span class="n">variant_predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
+        <span class="n">mode_of_inheritance_data</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">autosomal_dominant</span><span class="p">(),</span>
+    <span class="p">)</span></div>
+
+
 
-    <span class="n">MITOCHONDRIAL</span> <span class="o">=</span> <span class="mi">2</span>
+<div class="viewcode-block" id="autosomal_recessive">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_recessive">[docs]</a>
+<span class="k">def</span> <span class="nf">autosomal_recessive</span><span class="p">(</span>
+    <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">VariantPredicate</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Related to mitochondrial DNA.</span>
+<span class="sd">    Create a predicate that assigns the patient either into</span>
+<span class="sd">    homozygous reference, heterozygous, or biallelic alternative allele</span>
+<span class="sd">    (homozygous alternative or compound heterozygous)</span>
+<span class="sd">    group in line with the autosomal recessive mode of inheritance.</span>
+
+<span class="sd">    :param variant_predicate: a predicate for choosing the variants for testing</span>
+<span class="sd">        or `None` if all variants should be used</span>
 <span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">variant_predicate</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">variant_predicate</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">true</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">_from_moi_info</span><span class="p">(</span>
+        <span class="n">variant_predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
+        <span class="n">mode_of_inheritance_data</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">autosomal_recessive</span><span class="p">(),</span>
+    <span class="p">)</span></div>
+
+
+
+<span class="nd">@dataclasses</span><span class="o">.</span><span class="n">dataclass</span><span class="p">(</span><span class="n">eq</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">frozen</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<span class="k">class</span> <span class="nc">GenotypeGroup</span><span class="p">:</span>
+    <span class="n">allele_count</span><span class="p">:</span> <span class="nb">int</span>
+    <span class="n">sex</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">Sex</span><span class="p">]</span>
+    <span class="n">categorization</span><span class="p">:</span> <span class="n">Categorization</span>
 
 
 <span class="k">class</span> <span class="nc">ModeOfInheritanceInfo</span><span class="p">:</span>
@@ -424,13 +483,6 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
             <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Homozygous alternate or compound heterozygous&quot;</span><span class="p">,</span>
         <span class="p">),</span>
     <span class="p">)</span>
-    <span class="n">HEMI</span> <span class="o">=</span> <span class="n">Categorization</span><span class="p">(</span>
-        <span class="n">PatientCategory</span><span class="p">(</span>
-            <span class="n">cat_id</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span>
-            <span class="n">name</span><span class="o">=</span><span class="s2">&quot;HEMI&quot;</span><span class="p">,</span>
-            <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Hemizygous&quot;</span><span class="p">,</span>
-        <span class="p">),</span>
-    <span class="p">)</span>
 
     <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">autosomal_dominant</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritanceInfo&quot;</span><span class="p">:</span>
@@ -447,7 +499,6 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
             <span class="p">),</span>
         <span class="p">)</span>
         <span class="k">return</span> <span class="n">ModeOfInheritanceInfo</span><span class="p">(</span>
-            <span class="n">mendelian_inheritance_aspect</span><span class="o">=</span><span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">AUTOSOMAL</span><span class="p">,</span>
             <span class="n">groups</span><span class="o">=</span><span class="n">groups</span><span class="p">,</span>
         <span class="p">)</span>
 
@@ -471,62 +522,11 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
             <span class="p">),</span>
         <span class="p">)</span>
         <span class="k">return</span> <span class="n">ModeOfInheritanceInfo</span><span class="p">(</span>
-            <span class="n">mendelian_inheritance_aspect</span><span class="o">=</span><span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">AUTOSOMAL</span><span class="p">,</span>
-            <span class="n">groups</span><span class="o">=</span><span class="n">groups</span><span class="p">,</span>
-        <span class="p">)</span>
-
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">x_dominant</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritanceInfo&quot;</span><span class="p">:</span>
-        <span class="n">groups</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="n">GenotypeGroup</span><span class="p">(</span>
-                <span class="n">allele_count</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
-                <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-                <span class="n">categorization</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">HOM_REF</span><span class="p">,</span>
-            <span class="p">),</span>
-            <span class="n">GenotypeGroup</span><span class="p">(</span>
-                <span class="n">allele_count</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
-                <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-                <span class="n">categorization</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">HET</span><span class="p">,</span>
-            <span class="p">),</span>
-        <span class="p">)</span>
-        <span class="k">return</span> <span class="n">ModeOfInheritanceInfo</span><span class="p">(</span>
-            <span class="n">mendelian_inheritance_aspect</span><span class="o">=</span><span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">GONOSOMAL</span><span class="p">,</span>
-            <span class="n">groups</span><span class="o">=</span><span class="n">groups</span><span class="p">,</span>
-        <span class="p">)</span>
-
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">x_recessive</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritanceInfo&quot;</span><span class="p">:</span>
-        <span class="n">groups</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="n">GenotypeGroup</span><span class="p">(</span>
-                <span class="n">allele_count</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
-                <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-                <span class="n">categorization</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">HOM_REF</span><span class="p">,</span>
-            <span class="p">),</span>
-            <span class="n">GenotypeGroup</span><span class="p">(</span>
-                <span class="n">allele_count</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
-                <span class="n">sex</span><span class="o">=</span><span class="n">Sex</span><span class="o">.</span><span class="n">FEMALE</span><span class="p">,</span>
-                <span class="n">categorization</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">HET</span><span class="p">,</span>
-            <span class="p">),</span>
-            <span class="n">GenotypeGroup</span><span class="p">(</span>
-                <span class="n">allele_count</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
-                <span class="n">sex</span><span class="o">=</span><span class="n">Sex</span><span class="o">.</span><span class="n">FEMALE</span><span class="p">,</span>
-                <span class="n">categorization</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">BIALLELIC_ALT</span><span class="p">,</span>
-            <span class="p">),</span>
-            <span class="n">GenotypeGroup</span><span class="p">(</span>
-                <span class="n">allele_count</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
-                <span class="n">sex</span><span class="o">=</span><span class="n">Sex</span><span class="o">.</span><span class="n">MALE</span><span class="p">,</span>
-                <span class="n">categorization</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">HEMI</span><span class="p">,</span>
-            <span class="p">),</span>
-        <span class="p">)</span>
-
-        <span class="k">return</span> <span class="n">ModeOfInheritanceInfo</span><span class="p">(</span>
-            <span class="n">mendelian_inheritance_aspect</span><span class="o">=</span><span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">GONOSOMAL</span><span class="p">,</span>
             <span class="n">groups</span><span class="o">=</span><span class="n">groups</span><span class="p">,</span>
         <span class="p">)</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
-        <span class="n">mendelian_inheritance_aspect</span><span class="p">:</span> <span class="n">MendelianInheritanceAspect</span><span class="p">,</span>
         <span class="n">groups</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Iterable</span><span class="p">[</span><span class="n">GenotypeGroup</span><span class="p">],</span>
     <span class="p">):</span>
         <span class="c1"># We want this to be hashable but also keep a non-hashable dict</span>
@@ -534,10 +534,6 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="c1"># The correctness depends on two default dicts with same keys and values</span>
         <span class="c1"># comparing equal.</span>
         <span class="n">hash_value</span> <span class="o">=</span> <span class="mi">17</span>
-        <span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">mendelian_inheritance_aspect</span><span class="p">,</span> <span class="n">MendelianInheritanceAspect</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span> <span class="o">=</span> <span class="n">mendelian_inheritance_aspect</span>
-
-        <span class="n">hash_value</span> <span class="o">+=</span> <span class="mi">31</span> <span class="o">*</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">_groups</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
         <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
@@ -552,10 +548,6 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="c1"># Flatten `values()` which is an iterable of lists.</span>
         <span class="k">return</span> <span class="p">(</span><span class="n">group</span> <span class="k">for</span> <span class="n">meta_group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_groups</span><span class="o">.</span><span class="n">values</span><span class="p">()</span> <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">meta_group</span><span class="p">)</span>
 
-    <span class="nd">@property</span>
-    <span class="k">def</span> <span class="nf">mendelian_inheritance_aspect</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">MendelianInheritanceAspect</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span>
-
     <span class="k">def</span> <span class="nf">get_groups_for_allele_count</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">allele_count</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
@@ -566,19 +558,9 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
             <span class="c1"># No group for this allele count is OK</span>
             <span class="k">return</span> <span class="p">()</span>
 
-    <span class="k">def</span> <span class="nf">is_autosomal</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span> <span class="o">==</span> <span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">AUTOSOMAL</span>
-
-    <span class="k">def</span> <span class="nf">is_gonosomal</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span> <span class="o">==</span> <span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">GONOSOMAL</span>
-
-    <span class="k">def</span> <span class="nf">is_mitochondrial</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span> <span class="o">==</span> <span class="n">MendelianInheritanceAspect</span><span class="o">.</span><span class="n">MITOCHONDRIAL</span>
-
     <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
         <span class="k">return</span> <span class="p">(</span>
             <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">ModeOfInheritanceInfo</span><span class="p">)</span>
-            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_aspect</span>
             <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_groups</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_groups</span>
         <span class="p">)</span>
 
@@ -586,7 +568,7 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hash</span>
 
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;ModeOfInheritanceInfo(aspect=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_aspect</span><span class="si">}</span><span class="s2">, groups=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_groups</span><span class="si">}</span><span class="s2">)&quot;</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;ModeOfInheritanceInfo(groups=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_groups</span><span class="si">}</span><span class="s2">)&quot;</span>
 
     <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
         <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
@@ -604,8 +586,8 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
 <a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant">[docs]</a>
     <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">autosomal_dominant</span><span class="p">(</span>
-        <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritancePredicate&quot;</span><span class="p">:</span>
+        <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">VariantPredicate</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Create a predicate that assigns the patient either</span>
 <span class="sd">        into homozygous reference or heterozygous</span>
@@ -613,18 +595,21 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
 
 <span class="sd">        :param variant_predicate: a predicate for choosing the variants for testing.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">from_moi_info</span><span class="p">(</span>
-            <span class="n">variant_predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
-            <span class="n">mode_of_inheritance_data</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">autosomal_dominant</span><span class="p">(),</span>
-        <span class="p">)</span></div>
+        <span class="c1"># TODO: remove before 1.0.0</span>
+        <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
+            <span class="s2">&quot;Use `gpsea.analysis.predicate.genotype.autosomal_dominant` instead&quot;</span><span class="p">,</span>
+            <span class="ne">DeprecationWarning</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">autosomal_dominant</span><span class="p">(</span><span class="n">variant_predicate</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="ModeOfInheritancePredicate.autosomal_recessive">
 <a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive">[docs]</a>
     <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">autosomal_recessive</span><span class="p">(</span>
-        <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritancePredicate&quot;</span><span class="p">:</span>
+        <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">VariantPredicate</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenotypePolyPredicate</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Create a predicate that assigns the patient either into</span>
 <span class="sd">        homozygous reference, heterozygous, or biallelic alternative allele</span>
@@ -633,55 +618,17 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
 
 <span class="sd">        :param variant_predicate: a predicate for choosing the variants for testing.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">from_moi_info</span><span class="p">(</span>
-            <span class="n">variant_predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
-            <span class="n">mode_of_inheritance_data</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">autosomal_recessive</span><span class="p">(),</span>
-        <span class="p">)</span></div>
-
-
-<div class="viewcode-block" id="ModeOfInheritancePredicate.x_dominant">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant">[docs]</a>
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">x_dominant</span><span class="p">(</span>
-        <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritancePredicate&quot;</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Create a predicate that assigns the patient either into</span>
-<span class="sd">        homozygous reference or heterozygous</span>
-<span class="sd">        group in line with the X-linked dominant mode of inheritance.</span>
-
-<span class="sd">        :param variant_predicate: a predicate for choosing the variants for testing.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">from_moi_info</span><span class="p">(</span>
-            <span class="n">variant_predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
-            <span class="n">mode_of_inheritance_data</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">x_dominant</span><span class="p">(),</span>
-        <span class="p">)</span></div>
-
-
-<div class="viewcode-block" id="ModeOfInheritancePredicate.x_recessive">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive">[docs]</a>
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">x_recessive</span><span class="p">(</span>
-        <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritancePredicate&quot;</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Create a predicate that assigns the patient either into</span>
-<span class="sd">        homozygous reference, heterozygous, biallelic alternative allele</span>
-<span class="sd">        (homozygous alternative or compound heterozygous), or hemizygous</span>
-<span class="sd">        group in line with the X-linked recessive mode of inheritance.</span>
+        <span class="c1"># TODO: remove before 1.0.0</span>
+        <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
+            <span class="s2">&quot;Use `gpsea.analysis.predicate.genotype.autosomal_recessive` instead&quot;</span><span class="p">,</span>
+            <span class="ne">DeprecationWarning</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+        <span class="p">)</span>
 
-<span class="sd">        :param variant_predicate: a predicate for choosing the variants for testing.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">from_moi_info</span><span class="p">(</span>
-            <span class="n">variant_predicate</span><span class="o">=</span><span class="n">variant_predicate</span><span class="p">,</span>
-            <span class="n">mode_of_inheritance_data</span><span class="o">=</span><span class="n">ModeOfInheritanceInfo</span><span class="o">.</span><span class="n">x_recessive</span><span class="p">(),</span>
-        <span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">autosomal_recessive</span><span class="p">(</span><span class="n">variant_predicate</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="ModeOfInheritancePredicate.from_moi_info">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.from_moi_info">[docs]</a>
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">from_moi_info</span><span class="p">(</span>
+    <span class="k">def</span> <span class="nf">_from_moi_info</span><span class="p">(</span>
         <span class="n">variant_predicate</span><span class="p">:</span> <span class="n">VariantPredicate</span><span class="p">,</span>
         <span class="n">mode_of_inheritance_data</span><span class="p">:</span> <span class="n">ModeOfInheritanceInfo</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;ModeOfInheritancePredicate&quot;</span><span class="p">:</span>
@@ -692,8 +639,7 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="k">return</span> <span class="n">ModeOfInheritancePredicate</span><span class="p">(</span>
             <span class="n">allele_counter</span><span class="o">=</span><span class="n">allele_counter</span><span class="p">,</span>
             <span class="n">mode_of_inheritance_info</span><span class="o">=</span><span class="n">mode_of_inheritance_data</span><span class="p">,</span>
-        <span class="p">)</span></div>
-
+        <span class="p">)</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
@@ -714,7 +660,7 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="p">)</span>
         <span class="k">if</span> <span class="n">issues</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Cannot create predicate: </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">issues</span><span class="p">)))</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_question</span> <span class="o">=</span> <span class="s2">&quot;Which genotype group does the patient fit in&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_question</span> <span class="o">=</span> <span class="s2">&quot;What is the genotype group&quot;</span>
 
 <div class="viewcode-block" id="ModeOfInheritancePredicate.get_categorizations">
 <a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.get_categorizations">[docs]</a>
@@ -736,41 +682,12 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_check_patient</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_moi_info</span><span class="o">.</span><span class="n">is_autosomal</span><span class="p">():</span>
-            <span class="n">allele_count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
-            <span class="n">groups</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_moi_info</span><span class="o">.</span><span class="n">get_groups_for_allele_count</span><span class="p">(</span><span class="n">allele_count</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-                <span class="k">return</span> <span class="n">groups</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">categorization</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">return</span> <span class="kc">None</span>
-        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_moi_info</span><span class="o">.</span><span class="n">is_gonosomal</span><span class="p">():</span>
-            <span class="k">if</span> <span class="n">patient</span><span class="o">.</span><span class="n">sex</span><span class="o">.</span><span class="n">is_provided</span><span class="p">():</span>
-                <span class="n">allele_count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
-                <span class="n">groups</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_moi_info</span><span class="o">.</span><span class="n">get_groups_for_allele_count</span><span class="p">(</span><span class="n">allele_count</span><span class="p">)</span>
-                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                    <span class="c1"># Unable to assign the individual.</span>
-                    <span class="k">return</span> <span class="kc">None</span>
-                <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-                    <span class="c1"># We can only assign into one category no matter what the individual&#39;s sex is.</span>
-                    <span class="k">return</span> <span class="n">groups</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">categorization</span>
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="c1"># We choose depending on the sex.</span>
-                    <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
-                        <span class="k">if</span> <span class="n">group</span><span class="o">.</span><span class="n">sex</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">group</span><span class="o">.</span><span class="n">sex</span> <span class="o">==</span> <span class="n">patient</span><span class="o">.</span><span class="n">sex</span><span class="p">:</span>
-                            <span class="k">return</span> <span class="n">group</span><span class="o">.</span><span class="n">categorization</span>
-                <span class="k">return</span> <span class="kc">None</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="c1"># We must have patient&#39;s sex</span>
-                <span class="c1"># to do any meaningful analysis</span>
-                <span class="c1"># in the non-autosomal scenario.</span>
-                <span class="k">return</span> <span class="kc">None</span>
-
-        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_moi_info</span><span class="o">.</span><span class="n">is_mitochondrial</span><span class="p">():</span>
-            <span class="c1"># Cannot deal with mitochondrial inheritance right now.</span>
-            <span class="k">return</span> <span class="kc">None</span>
+        <span class="n">allele_count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allele_counter</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
+        <span class="n">groups</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_moi_info</span><span class="o">.</span><span class="n">get_groups_for_allele_count</span><span class="p">(</span><span class="n">allele_count</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">groups</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">categorization</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="c1"># Bug, please report to the developers</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected mode of inheritance condition&quot;</span><span class="p">)</span></div>
+            <span class="k">return</span> <span class="kc">None</span></div>
 
 
     <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
@@ -838,6 +755,12 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="k">else</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">None</span>
 
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">SexGenotypePredicate</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+        <span class="k">return</span> <span class="mi">31</span>
+
 
 <span class="n">INSTANCE</span> <span class="o">=</span> <span class="n">SexGenotypePredicate</span><span class="p">()</span>
 
@@ -848,7 +771,7 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Get a genotype predicate for categorizing patients by their :class:`~gpsea.model.Sex`.</span>
 
-<span class="sd">    See the :ref:`sex-predicate` section for an example.</span>
+<span class="sd">    See the :ref:`male-female-predicate` section for an example.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="n">INSTANCE</span></div>
 
@@ -870,7 +793,7 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
                 <span class="k">pass</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2"> is neither `str` nor `hpotk.TermId`&quot;</span><span class="p">)</span>
-            
+
             <span class="n">diagnosis_ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">labels</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -904,12 +827,13 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
         <span class="bp">self</span><span class="o">.</span><span class="n">_categorizations</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
             <span class="nb">sorted</span><span class="p">(</span><span class="n">categorizations</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">c</span><span class="p">:</span> <span class="n">c</span><span class="o">.</span><span class="n">category</span><span class="o">.</span><span class="n">cat_id</span><span class="p">)</span>
         <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_hash</span> <span class="o">=</span> <span class="nb">hash</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">categorizations</span><span class="o">.</span><span class="n">items</span><span class="p">()))</span>
 
     <span class="k">def</span> <span class="nf">get_categorizations</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_categorizations</span>
 
     <span class="k">def</span> <span class="nf">get_question_base</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="s1">&#39;What disease was diagnosed&#39;</span>
+        <span class="k">return</span> <span class="s2">&quot;What disease was diagnosed&quot;</span>
 
     <span class="k">def</span> <span class="nf">test</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">patient</span><span class="p">:</span> <span class="n">Patient</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">Categorization</span><span class="p">]:</span>
         <span class="n">categorization</span> <span class="o">=</span> <span class="kc">None</span>
@@ -919,15 +843,22 @@ <h1>Source code for gpsea.analysis.predicate.genotype._gt_predicates</h1><div cl
             <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
                 <span class="c1"># No match for this disease, no problem.</span>
                 <span class="k">continue</span>
-            
+
             <span class="k">if</span> <span class="n">categorization</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                 <span class="c1"># First time we found a candidate disease</span>
                 <span class="n">categorization</span> <span class="o">=</span> <span class="n">candidate</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="c1"># Ambiguous match. We found several matching diagnoses!</span>
                 <span class="k">return</span> <span class="kc">None</span>
-                
+
         <span class="k">return</span> <span class="n">categorization</span>
+    
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">DiagnosisPredicate</span><span class="p">)</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_id2cat</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_id2cat</span>
+    
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hash</span>
 
 
 <div class="viewcode-block" id="diagnosis_predicate">
diff --git a/stable/_modules/gpsea/analysis/predicate/genotype/_variant.html b/stable/_modules/gpsea/analysis/predicate/genotype/_variant.html
index be22afcd1..49cb29109 100644
--- a/stable/_modules/gpsea/analysis/predicate/genotype/_variant.html
+++ b/stable/_modules/gpsea/analysis/predicate/genotype/_variant.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.genotype._variant &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.genotype._variant &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
@@ -103,6 +103,17 @@ <h1>Source code for gpsea.analysis.predicate.genotype._variant</h1><div class="h
 <span class="sd">    that are relatively simple to configure.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
+<div class="viewcode-block" id="VariantPredicates.true">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates.true">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">true</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">VariantPredicate</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Prepare an absolutely inclusive :class:`VariantPredicate` - a predicate that returns `True`</span>
+<span class="sd">        for any variant whatsoever.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">AlwaysTrueVariantPredicate</span><span class="o">.</span><span class="n">get_instance</span><span class="p">()</span></div>
+
+
 <div class="viewcode-block" id="VariantPredicates.all">
 <a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates.all">[docs]</a>
     <span class="nd">@staticmethod</span>
@@ -245,6 +256,21 @@ <h1>Source code for gpsea.analysis.predicate.genotype._variant</h1><div class="h
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Prepare a :class:`VariantPredicate` that tests if the variant overlaps with an exon of a specific transcript.</span>
 
+<span class="sd">        .. warning::</span>
+
+<span class="sd">            We use 1-based numbering to number the exons,</span>
+<span class="sd">            not the usual 0-based numbering of the computer science.</span>
+<span class="sd">            Therefore, the first exon of the transcript</span>
+<span class="sd">            has ``exon_number==1``, the second exon is ``2``, and so on ...</span>
+
+<span class="sd">        .. warning::</span>
+
+<span class="sd">            We do not check if the `exon_number` spans</span>
+<span class="sd">            beyond the number of exons of the given `transcript_id`!</span>
+<span class="sd">            Therefore, ``exon_number==10,000`` will effectively return `False`</span>
+<span class="sd">            for *all* variants!!! 😱</span>
+<span class="sd">            Well, at least the genome variants of the *Homo sapiens sapiens* taxon...</span>
+
 <span class="sd">        Args:</span>
 <span class="sd">            exon: a non-negative `int` with the index of the target exon</span>
 <span class="sd">                (e.g. `0` for the 1st exon, `1` for the 2nd, ...)</span>
diff --git a/stable/_modules/gpsea/analysis/predicate/phenotype/_pheno.html b/stable/_modules/gpsea/analysis/predicate/phenotype/_pheno.html
index 0f840efce..4ebad97d9 100644
--- a/stable/_modules/gpsea/analysis/predicate/phenotype/_pheno.html
+++ b/stable/_modules/gpsea/analysis/predicate/phenotype/_pheno.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.phenotype._pheno &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.phenotype._pheno &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
@@ -181,15 +181,17 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._pheno</h1><div class="hi
 
 
 
-<div class="viewcode-block" id="PropagatingPhenotypePredicate">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate">[docs]</a>
-<span class="k">class</span> <span class="nc">PropagatingPhenotypePredicate</span><span class="p">(</span><span class="n">PhenotypePolyPredicate</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">]):</span>
+<div class="viewcode-block" id="HpoPredicate">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate">[docs]</a>
+<span class="k">class</span> <span class="nc">HpoPredicate</span><span class="p">(</span><span class="n">PhenotypePolyPredicate</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">]):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    `PropagatingPhenotypePredicate` tests if a patient is annotated with an HPO term.</span>
+<span class="sd">    `HpoPredicate` tests if a patient is annotated with an HPO term.</span>
 
 <span class="sd">    Note, `query` must be a term of the provided `hpo`!</span>
 
-<span class="sd">    :param hpo: HPO object</span>
+<span class="sd">    See :ref:`hpo-predicate` section for an example usage.</span>
+
+<span class="sd">    :param hpo: HPO ontology</span>
 <span class="sd">    :param query: the HPO term to test</span>
 <span class="sd">    :param missing_implies_phenotype_excluded: `True` if lack of an explicit annotation implies term&#39;s absence`.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -222,8 +224,8 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._pheno</h1><div class="hi
         <span class="c1"># Some tests depend on the order of `self._categorizations`.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_categorizations</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_phenotype_observed</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phenotype_excluded</span><span class="p">)</span>
 
-<div class="viewcode-block" id="PropagatingPhenotypePredicate.get_question_base">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_question_base">[docs]</a>
+<div class="viewcode-block" id="HpoPredicate.get_question_base">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.get_question_base">[docs]</a>
     <span class="k">def</span> <span class="nf">get_question_base</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
         <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;Is </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_query_label</span><span class="si">}</span><span class="s2"> present in the patient&quot;</span></div>
 
@@ -236,16 +238,16 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._pheno</h1><div class="hi
     <span class="k">def</span> <span class="nf">present_phenotype_categorization</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">PhenotypeCategorization</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">]:</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phenotype_observed</span>
 
-<div class="viewcode-block" id="PropagatingPhenotypePredicate.get_categorizations">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_categorizations">[docs]</a>
+<div class="viewcode-block" id="HpoPredicate.get_categorizations">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.get_categorizations">[docs]</a>
     <span class="k">def</span> <span class="nf">get_categorizations</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">PhenotypeCategorization</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">]]:</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_categorizations</span></div>
 
 
-<div class="viewcode-block" id="PropagatingPhenotypePredicate.test">
-<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.test">[docs]</a>
+<div class="viewcode-block" id="HpoPredicate.test">
+<a class="viewcode-back" href="../../../../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.test">[docs]</a>
     <span class="k">def</span> <span class="nf">test</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span> <span class="n">patient</span><span class="p">:</span> <span class="n">Patient</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">PhenotypeCategorization</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">]]:</span>
@@ -295,8 +297,17 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._pheno</h1><div class="hi
         <span class="k">return</span> <span class="kc">None</span></div>
 
 
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">HpoPredicate</span><span class="p">)</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_hpo</span><span class="o">.</span><span class="n">version</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_hpo</span><span class="o">.</span><span class="n">version</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_query</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_missing_implies_phenotype_excluded</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_missing_implies_phenotype_excluded</span>
+    
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">_hpo</span><span class="o">.</span><span class="n">version</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_missing_implies_phenotype_excluded</span><span class="p">))</span>
+
     <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;PropagatingPhenotypeBooleanPredicate(query=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_query</span><span class="si">}</span><span class="s2">)&quot;</span></div>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;HpoPredicate(query=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_query</span><span class="si">}</span><span class="s2">)&quot;</span></div>
 
 
 
@@ -374,6 +385,13 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._pheno</h1><div class="hi
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_diagnosis_excluded</span></div>
 
 
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">object</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">DiseasePresencePredicate</span><span class="p">)</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query</span> <span class="o">==</span> <span class="n">value</span><span class="o">.</span><span class="n">_query</span>
+    
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">_query</span><span class="p">,))</span>
+
     <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;DiseasePresencePredicate(query=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_query</span><span class="si">}</span><span class="s2">)&quot;</span></div>
 
diff --git a/stable/_modules/gpsea/analysis/predicate/phenotype/_util.html b/stable/_modules/gpsea/analysis/predicate/phenotype/_util.html
index 93f784699..87ed7ab73 100644
--- a/stable/_modules/gpsea/analysis/predicate/phenotype/_util.html
+++ b/stable/_modules/gpsea/analysis/predicate/phenotype/_util.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.phenotype._util &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.phenotype._util &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../../search.html" method="get">
@@ -87,7 +87,7 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._util</h1><div class="hig
 
 <span class="kn">import</span> <span class="nn">hpotk</span>
 
-<span class="kn">from</span> <span class="nn">._pheno</span> <span class="kn">import</span> <span class="n">PhenotypePolyPredicate</span><span class="p">,</span> <span class="n">PropagatingPhenotypePredicate</span>
+<span class="kn">from</span> <span class="nn">._pheno</span> <span class="kn">import</span> <span class="n">PhenotypePolyPredicate</span><span class="p">,</span> <span class="n">HpoPredicate</span>
 
 <span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">Patient</span>
 
@@ -111,7 +111,7 @@ <h1>Source code for gpsea.analysis.predicate.phenotype._util</h1><div class="hig
 <span class="sd">        (either directly or indirectly) for the term to be included in the analysis.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
-        <span class="n">PropagatingPhenotypePredicate</span><span class="p">(</span>
+        <span class="n">HpoPredicate</span><span class="p">(</span>
             <span class="n">hpo</span><span class="o">=</span><span class="n">hpo</span><span class="p">,</span>
             <span class="n">query</span><span class="o">=</span><span class="n">term</span><span class="p">,</span>
             <span class="n">missing_implies_phenotype_excluded</span><span class="o">=</span><span class="n">missing_implies_excluded</span><span class="p">,</span>
diff --git a/stable/_modules/gpsea/analysis/pscore/_api.html b/stable/_modules/gpsea/analysis/pscore/_api.html
index 44309e2dd..6053d9b20 100644
--- a/stable/_modules/gpsea/analysis/pscore/_api.html
+++ b/stable/_modules/gpsea/analysis/pscore/_api.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pscore._api &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pscore._api &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
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diff --git a/stable/_modules/gpsea/analysis/pscore/_impl.html b/stable/_modules/gpsea/analysis/pscore/_impl.html
index 33dcf1893..09e72e225 100644
--- a/stable/_modules/gpsea/analysis/pscore/_impl.html
+++ b/stable/_modules/gpsea/analysis/pscore/_impl.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pscore._impl &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pscore._impl &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
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@@ -16,7 +16,7 @@
   
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -38,7 +38,7 @@
             GPSEA
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diff --git a/stable/_modules/gpsea/analysis/pscore/stats/_stats.html b/stable/_modules/gpsea/analysis/pscore/stats/_stats.html
index 49c3c2af9..1b34509ac 100644
--- a/stable/_modules/gpsea/analysis/pscore/stats/_stats.html
+++ b/stable/_modules/gpsea/analysis/pscore/stats/_stats.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pscore.stats._stats &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pscore.stats._stats &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -38,7 +38,7 @@
             GPSEA
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+                0.4
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diff --git a/stable/_modules/gpsea/config.html b/stable/_modules/gpsea/config.html
index b3c1fc453..02b3c9334 100644
--- a/stable/_modules/gpsea/config.html
+++ b/stable/_modules/gpsea/config.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.config &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.config &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../_static/doctools.js?v=9a2dae69"></script>
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@@ -38,7 +38,7 @@
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diff --git a/stable/_modules/gpsea/data/_toy.html b/stable/_modules/gpsea/data/_toy.html
deleted file mode 100644
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--- a/stable/_modules/gpsea/data/_toy.html
+++ /dev/null
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-<!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../../">
-<head>
-  <meta charset="utf-8" />
-  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.data._toy &mdash; GPSEA 0.3.0 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
-      <link rel="stylesheet" type="text/css" href="../../../_static/gpsea.css?v=547657ed" />
-
-  
-  <!--[if lt IE 9]>
-    <script src="../../../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
-  
-        <script src="../../../_static/jquery.js?v=5d32c60e"></script>
-        <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
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-  <h1>Source code for gpsea.data._toy</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">hpotk</span> <span class="kn">import</span> <span class="n">TermId</span>
-
-<span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">gpsea.model.genome</span> <span class="kn">import</span> <span class="n">Contig</span><span class="p">,</span> <span class="n">GenomicRegion</span><span class="p">,</span> <span class="n">Strand</span>
-
-<span class="n">CONTIG</span> <span class="o">=</span> <span class="n">Contig</span><span class="p">(</span><span class="s2">&quot;1&quot;</span><span class="p">,</span> <span class="s2">&quot;GB_ACC&quot;</span><span class="p">,</span> <span class="s2">&quot;REFSEQ_NAME&quot;</span><span class="p">,</span> <span class="s2">&quot;UCSC_NAME&quot;</span><span class="p">,</span> <span class="mi">1_000</span><span class="p">)</span>
-
-
-<span class="k">def</span> <span class="nf">make_region</span><span class="p">(</span><span class="n">start</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">end</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GenomicRegion</span><span class="p">:</span>
-    <span class="k">return</span> <span class="n">GenomicRegion</span><span class="p">(</span><span class="n">CONTIG</span><span class="p">,</span> <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">Strand</span><span class="o">.</span><span class="n">POSITIVE</span><span class="p">)</span>
-
-
-<div class="viewcode-block" id="get_toy_cohort">
-<a class="viewcode-back" href="../../../apidocs/gpsea.data.html#gpsea.data.get_toy_cohort">[docs]</a>
-<span class="k">def</span> <span class="nf">get_toy_cohort</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Cohort</span><span class="p">:</span>
-    <span class="c1"># TODO - Lauren - implement sample patients from the terms below</span>
-    <span class="c1"># - Arachnodactyly HP:0001166</span>
-    <span class="c1"># - Focal clonic seizure HP:0002266</span>
-    <span class="c1"># - Perimembranous ventricular septal defect HP:0011682</span>
-    <span class="c1"># - Hepatosplenomegaly HP:0001433</span>
-    <span class="c1"># - Tubularization of Bowman capsule HP:0032648</span>
-    <span class="c1"># - Intercostal muscle weakness HP:0004878</span>
-    <span class="c1"># - Enuresis nocturna HP:0010677</span>
-    <span class="c1"># - Spasticity HP:0001257</span>
-    <span class="c1"># - Chronic pancreatitis HP:0006280</span>
-
-    <span class="n">arachnodactyly_T</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0001166&quot;</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="n">focal_clonic_seizure_T</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0002266&quot;</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="n">seizure_T</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0001250&quot;</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="n">spasticity_T</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0001257&quot;</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="n">arachnodactyly_F</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0001166&quot;</span><span class="p">),</span> <span class="kc">False</span><span class="p">)</span>
-    <span class="n">focal_clonic_seizure_F</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0002266&quot;</span><span class="p">),</span> <span class="kc">False</span><span class="p">)</span>
-    <span class="n">seizure_F</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0001250&quot;</span><span class="p">),</span> <span class="kc">False</span><span class="p">)</span>
-    <span class="n">spasticity_F</span> <span class="o">=</span> <span class="n">Phenotype</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;HP:0001257&quot;</span><span class="p">),</span> <span class="kc">False</span><span class="p">)</span>
-
-    <span class="n">Disease_T</span> <span class="o">=</span> <span class="n">Disease</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;OMIM:001234&quot;</span><span class="p">),</span> <span class="s2">&quot;Test present disease&quot;</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="n">Disease_F</span> <span class="o">=</span> <span class="n">Disease</span><span class="p">(</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s2">&quot;OMIM:001234&quot;</span><span class="p">),</span> <span class="s2">&quot;Test absent disease&quot;</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
-
-    <span class="n">snv</span> <span class="o">=</span> <span class="n">Variant</span><span class="o">.</span><span class="n">create_variant_from_scratch</span><span class="p">(</span>
-        <span class="n">VariantCoordinates</span><span class="p">(</span><span class="n">make_region</span><span class="p">(</span><span class="mi">280</span><span class="p">,</span> <span class="mi">281</span><span class="p">),</span> <span class="s2">&quot;A&quot;</span><span class="p">,</span> <span class="s2">&quot;G&quot;</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
-        <span class="s2">&quot;FakeGene&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5:c.180A&gt;G&quot;</span><span class="p">,</span>
-        <span class="kc">False</span><span class="p">,</span>
-        <span class="p">[</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">],</span>
-        <span class="p">[</span><span class="mi">1</span><span class="p">],</span>
-        <span class="s2">&quot;NP_09876.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NP_09876.5:p.Unk200&quot;</span><span class="p">,</span>
-        <span class="mi">60</span><span class="p">,</span>
-        <span class="mi">60</span><span class="p">,</span>
-        <span class="n">Genotypes</span><span class="o">.</span><span class="n">from_mapping</span><span class="p">(</span>
-            <span class="p">{</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;A&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;B&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;C&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HOMOZYGOUS_ALTERNATE</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;D&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;E&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;G&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;J&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;K&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;M&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;N&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HOMOZYGOUS_ALTERNATE</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;P&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;Q&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HOMOZYGOUS_ALTERNATE</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;R&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;T&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;V&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;Y&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-            <span class="p">}</span>
-        <span class="p">),</span>
-    <span class="p">)</span>
-    <span class="n">deletion</span> <span class="o">=</span> <span class="n">Variant</span><span class="o">.</span><span class="n">create_variant_from_scratch</span><span class="p">(</span>
-        <span class="n">VariantCoordinates</span><span class="p">(</span><span class="n">make_region</span><span class="p">(</span><span class="mi">360</span><span class="p">,</span> <span class="mi">363</span><span class="p">),</span> <span class="s2">&quot;TTC&quot;</span><span class="p">,</span> <span class="s2">&quot;T&quot;</span><span class="p">,</span> <span class="o">-</span><span class="mi">2</span><span class="p">),</span>
-        <span class="s2">&quot;FakeGene&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5:c.261_263del&quot;</span><span class="p">,</span>
-        <span class="kc">False</span><span class="p">,</span>
-        <span class="p">[</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">],</span>
-        <span class="p">[</span><span class="mi">2</span><span class="p">],</span>
-        <span class="s2">&quot;NP_09876.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NP_09876.5:p.Unk200&quot;</span><span class="p">,</span>
-        <span class="mi">86</span><span class="p">,</span>
-        <span class="mi">87</span><span class="p">,</span>
-        <span class="n">Genotypes</span><span class="o">.</span><span class="n">from_mapping</span><span class="p">(</span>
-            <span class="p">{</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;D&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;F&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;G&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;H&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;I&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HOMOZYGOUS_ALTERNATE</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;L&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;O&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;R&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;S&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HOMOZYGOUS_ALTERNATE</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;U&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;W&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;X&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-                <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;Z&quot;</span><span class="p">):</span> <span class="n">Genotype</span><span class="o">.</span><span class="n">HETEROZYGOUS</span><span class="p">,</span>
-            <span class="p">}</span>
-        <span class="p">),</span>
-    <span class="p">)</span>
-    <span class="n">het_dup</span> <span class="o">=</span> <span class="n">Variant</span><span class="o">.</span><span class="n">create_variant_from_scratch</span><span class="p">(</span>
-        <span class="n">VariantCoordinates</span><span class="p">(</span><span class="n">make_region</span><span class="p">(</span><span class="mi">175</span><span class="p">,</span> <span class="mi">176</span><span class="p">),</span> <span class="s2">&quot;T&quot;</span><span class="p">,</span> <span class="s2">&quot;TG&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
-        <span class="s2">&quot;FakeGene&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5:c.75A&gt;G&quot;</span><span class="p">,</span>
-        <span class="kc">False</span><span class="p">,</span>
-        <span class="p">[</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">],</span>
-        <span class="p">[</span><span class="mi">1</span><span class="p">],</span>
-        <span class="s2">&quot;NP_09876.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NP_09876.5:p.Unk200&quot;</span><span class="p">,</span>
-        <span class="mi">25</span><span class="p">,</span>
-        <span class="mi">25</span><span class="p">,</span>
-        <span class="n">Genotypes</span><span class="o">.</span><span class="n">empty</span><span class="p">(),</span>
-    <span class="p">)</span>  <span class="c1"># Not used in the patients below, hence `empty()`.</span>
-    <span class="n">hom_dup</span> <span class="o">=</span> <span class="n">Variant</span><span class="o">.</span><span class="n">create_variant_from_scratch</span><span class="p">(</span>
-        <span class="n">VariantCoordinates</span><span class="p">(</span><span class="n">make_region</span><span class="p">(</span><span class="mi">175</span><span class="p">,</span> <span class="mi">176</span><span class="p">),</span> <span class="s2">&quot;T&quot;</span><span class="p">,</span> <span class="s2">&quot;TG&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
-        <span class="s2">&quot;FakeGene&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NM_1234.5:c.75A&gt;G&quot;</span><span class="p">,</span>
-        <span class="kc">False</span><span class="p">,</span>
-        <span class="p">[</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">],</span>
-        <span class="p">[</span><span class="mi">1</span><span class="p">],</span>
-        <span class="s2">&quot;NP_09876.5&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;NP_09876.5:p.Unk200&quot;</span><span class="p">,</span>
-        <span class="mi">25</span><span class="p">,</span>
-        <span class="mi">25</span><span class="p">,</span>
-        <span class="n">Genotypes</span><span class="o">.</span><span class="n">empty</span><span class="p">(),</span>
-    <span class="p">)</span>  <span class="c1"># Not used in the patients below, hence `empty()`.</span>
-
-    <span class="n">patients</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;A&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;B&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;C&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;D&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">,</span> <span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;E&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">,</span> <span class="n">seizure_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;F&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;G&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">,</span> <span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;H&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;I&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;J&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;K&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;L&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_F</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;M&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_F</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;N&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;O&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_F</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;P&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;Q&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_F</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;R&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_F</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">,</span> <span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;S&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;T&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_F</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;U&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;V&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;W&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;X&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;Y&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_T</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">snv</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-        <span class="n">Patient</span><span class="o">.</span><span class="n">from_raw_parts</span><span class="p">(</span>
-            <span class="n">SampleLabels</span><span class="p">(</span><span class="s2">&quot;Z&quot;</span><span class="p">),</span>
-            <span class="n">sex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-            <span class="n">phenotypes</span><span class="o">=</span><span class="p">(</span><span class="n">arachnodactyly_F</span><span class="p">,</span> <span class="n">seizure_T</span><span class="p">,</span> <span class="n">spasticity_T</span><span class="p">),</span>
-            <span class="n">variants</span><span class="o">=</span><span class="p">[</span><span class="n">deletion</span><span class="p">],</span>
-            <span class="n">diseases</span><span class="o">=</span><span class="p">[</span><span class="n">Disease_T</span><span class="p">],</span>
-        <span class="p">),</span>
-    <span class="p">)</span>
-
-    <span class="k">return</span> <span class="n">Cohort</span><span class="o">.</span><span class="n">from_patients</span><span class="p">(</span><span class="n">patients</span><span class="p">)</span></div>
-
-</pre></div>
-
-           </div>
-          </div>
-          <footer>
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>&#169; Copyright 2024.</p>
-  </div>
-
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
-    provided by <a href="https://readthedocs.org">Read the Docs</a>.
-   
-
-</footer>
-        </div>
-      </div>
-    </section>
-  </div>
-  <script>
-      jQuery(function () {
-          SphinxRtdTheme.Navigation.enable(true);
-      });
-  </script> 
-
-</body>
-</html>
\ No newline at end of file
diff --git a/stable/_modules/gpsea/io.html b/stable/_modules/gpsea/io.html
index 469f16dec..cd95fac0e 100644
--- a/stable/_modules/gpsea/io.html
+++ b/stable/_modules/gpsea/io.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.io &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.io &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_base.html b/stable/_modules/gpsea/model/_base.html
index c4fd134a2..d1c04ca8e 100644
--- a/stable/_modules/gpsea/model/_base.html
+++ b/stable/_modules/gpsea/model/_base.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._base &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._base &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_cohort.html b/stable/_modules/gpsea/model/_cohort.html
index 9a62174f4..510d535dc 100644
--- a/stable/_modules/gpsea/model/_cohort.html
+++ b/stable/_modules/gpsea/model/_cohort.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._cohort &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._cohort &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_gt.html b/stable/_modules/gpsea/model/_gt.html
index 6ca4b0f8b..e7a9fba1d 100644
--- a/stable/_modules/gpsea/model/_gt.html
+++ b/stable/_modules/gpsea/model/_gt.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._gt &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._gt &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_phenotype.html b/stable/_modules/gpsea/model/_phenotype.html
index 241c3bb15..82439c10c 100644
--- a/stable/_modules/gpsea/model/_phenotype.html
+++ b/stable/_modules/gpsea/model/_phenotype.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._phenotype &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._phenotype &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_protein.html b/stable/_modules/gpsea/model/_protein.html
index 8da9b0b50..8d1bade77 100644
--- a/stable/_modules/gpsea/model/_protein.html
+++ b/stable/_modules/gpsea/model/_protein.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._protein &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._protein &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_tx.html b/stable/_modules/gpsea/model/_tx.html
index bc883967c..983686f96 100644
--- a/stable/_modules/gpsea/model/_tx.html
+++ b/stable/_modules/gpsea/model/_tx.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._tx &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._tx &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_variant.html b/stable/_modules/gpsea/model/_variant.html
index e617f3625..d2362acf5 100644
--- a/stable/_modules/gpsea/model/_variant.html
+++ b/stable/_modules/gpsea/model/_variant.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._variant &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._variant &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/model/_variant_effects.html b/stable/_modules/gpsea/model/_variant_effects.html
index 8b61edcae..9a7364816 100644
--- a/stable/_modules/gpsea/model/_variant_effects.html
+++ b/stable/_modules/gpsea/model/_variant_effects.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model._variant_effects &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model._variant_effects &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
@@ -81,12 +81,15 @@
            <div itemprop="articleBody">
              
   <h1>Source code for gpsea.model._variant_effects</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">enum</span> <span class="kn">import</span> <span class="n">Enum</span>
+<span></span><span class="kn">import</span> <span class="nn">enum</span>
+<span class="kn">import</span> <span class="nn">typing</span>
+
+<span class="kn">import</span> <span class="nn">hpotk</span>
 
 
 <div class="viewcode-block" id="VariantEffect">
 <a class="viewcode-back" href="../../../apidocs/gpsea.model.html#gpsea.model.VariantEffect">[docs]</a>
-<span class="k">class</span> <span class="nc">VariantEffect</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">VariantEffect</span><span class="p">(</span><span class="n">enum</span><span class="o">.</span><span class="n">Enum</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    `VariantEffect` represents consequences of a variant on transcript that are supported by GPSEA.</span>
 
@@ -132,7 +135,7 @@ <h1>Source code for gpsea.model._variant_effects</h1><div class="highlight"><pre
     <span class="n">THREE_PRIME_UTR_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001624&quot;</span>
     <span class="n">NON_CODING_TRANSCRIPT_EXON_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001792&quot;</span>
     <span class="n">INTRON_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001627&quot;</span>
-    <span class="n">NMD_TRANSCRIPT_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001621&quot;</span><span class="p">,</span>
+    <span class="n">NMD_TRANSCRIPT_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001621&quot;</span>
     <span class="n">NON_CODING_TRANSCRIPT_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001619&quot;</span>
     <span class="n">UPSTREAM_GENE_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001631&quot;</span>
     <span class="n">DOWNSTREAM_GENE_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001632&quot;</span>
@@ -147,6 +150,49 @@ <h1>Source code for gpsea.model._variant_effects</h1><div class="highlight"><pre
     <span class="n">INTERGENIC_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001628&quot;</span>
     <span class="n">SEQUENCE_VARIANT</span> <span class="o">=</span> <span class="s2">&quot;SO:0001060&quot;</span>
 
+<div class="viewcode-block" id="VariantEffect.to_display">
+<a class="viewcode-back" href="../../../apidocs/gpsea.model.html#gpsea.model.VariantEffect.to_display">[docs]</a>
+    <span class="k">def</span> <span class="nf">to_display</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Get a concise name of the variant effect that is suitable for showing to humans.</span>
+
+<span class="sd">        Example</span>
+<span class="sd">        ^^^^^^^</span>
+
+<span class="sd">        &gt;&gt;&gt; from gpsea.model import VariantEffect</span>
+<span class="sd">        &gt;&gt;&gt; VariantEffect.MISSENSE_VARIANT.to_display()</span>
+<span class="sd">        &#39;missense&#39;</span>
+<span class="sd">        &gt;&gt;&gt; VariantEffect.SPLICE_DONOR_5TH_BASE_VARIANT.to_display()</span>
+<span class="sd">        &#39;splice donor 5th base&#39;</span>
+
+<span class="sd">        :returns: a `str` with the name or `&#39;n/a&#39;` if the variant effect was not assigned a concise name.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">effect_to_display</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s2">&quot;n/a&quot;</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="VariantEffect.structural_so_id_to_display">
+<a class="viewcode-back" href="../../../apidocs/gpsea.model.html#gpsea.model.VariantEffect.structural_so_id_to_display">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">structural_so_id_to_display</span><span class="p">(</span><span class="n">so_term</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Union</span><span class="p">[</span><span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">,</span> <span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Get a `str` with a concise name for representing a Sequence Ontology (SO) term identifier.</span>
+
+<span class="sd">        Example</span>
+<span class="sd">        ^^^^^^^</span>
+
+<span class="sd">        &gt;&gt;&gt; from gpsea.model import VariantEffect</span>
+<span class="sd">        &gt;&gt;&gt; VariantEffect.structural_so_id_to_display(&#39;SO:1000029&#39;)</span>
+<span class="sd">        &#39;chromosomal deletion&#39;</span>
+
+<span class="sd">        :param so_term: a CURIE `str` or a :class:`~hpotk.TermId` with the query SO term.</span>
+<span class="sd">        :returns: a `str` with the concise name for the SO term or `&#39;n/a&#39;` if a name has not been assigned yet.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">so_term</span><span class="p">,</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">):</span>
+            <span class="n">so_term</span> <span class="o">=</span> <span class="n">so_term</span><span class="o">.</span><span class="n">value</span>
+
+        <span class="k">return</span> <span class="n">so_id_to_display</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">so_term</span><span class="p">,</span> <span class="s2">&quot;n/a&quot;</span><span class="p">)</span></div>
+
+
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">curie</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_curie</span> <span class="o">=</span> <span class="n">curie</span>
 
@@ -161,6 +207,57 @@ <h1>Source code for gpsea.model._variant_effects</h1><div class="highlight"><pre
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span></div>
 
+
+
+<span class="n">effect_to_display</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">TRANSCRIPT_ABLATION</span><span class="p">:</span> <span class="s2">&quot;transcript ablation&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_ACCEPTOR_VARIANT</span><span class="p">:</span> <span class="s2">&quot;splice acceptor&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_VARIANT</span><span class="p">:</span> <span class="s2">&quot;splice donor&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_GAINED</span><span class="p">:</span> <span class="s2">&quot;stop gained&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">:</span> <span class="s2">&quot;frameshift&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_LOST</span><span class="p">:</span> <span class="s2">&quot;stop lost&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">START_LOST</span><span class="p">:</span> <span class="s2">&quot;start lost&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">TRANSCRIPT_AMPLIFICATION</span><span class="p">:</span> <span class="s2">&quot;transcript amplification&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INFRAME_INSERTION</span><span class="p">:</span> <span class="s2">&quot;inframe insertion&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INFRAME_DELETION</span><span class="p">:</span> <span class="s2">&quot;inframe deletion&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;missense&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">PROTEIN_ALTERING_VARIANT</span><span class="p">:</span> <span class="s2">&quot;protein altering&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_REGION_VARIANT</span><span class="p">:</span> <span class="s2">&quot;splice region&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_5TH_BASE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;splice donor 5th base&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_REGION_VARIANT</span><span class="p">:</span> <span class="s2">&quot;splice donor&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_POLYPYRIMIDINE_TRACT_VARIANT</span><span class="p">:</span> <span class="s2">&quot;splice polypyrimidine&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INCOMPLETE_TERMINAL_CODON_VARIANT</span><span class="p">:</span> <span class="s2">&quot;incomplete terminal codon&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">START_RETAINED_VARIANT</span><span class="p">:</span> <span class="s2">&quot;start retained&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_RETAINED_VARIANT</span><span class="p">:</span> <span class="s2">&quot;stop retainined&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SYNONYMOUS_VARIANT</span><span class="p">:</span> <span class="s2">&quot;synonymous&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">CODING_SEQUENCE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;coding sequence&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">MATURE_MIRNA_VARIANT</span><span class="p">:</span> <span class="s2">&quot;mature miRNA&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">FIVE_PRIME_UTR_VARIANT</span><span class="p">:</span> <span class="s2">&quot;5UTR&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">THREE_PRIME_UTR_VARIANT</span><span class="p">:</span> <span class="s2">&quot;3UTR&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">NON_CODING_TRANSCRIPT_EXON_VARIANT</span><span class="p">:</span> <span class="s2">&quot;non-coding transcript exon&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INTRON_VARIANT</span><span class="p">:</span> <span class="s2">&quot;intronic&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">NMD_TRANSCRIPT_VARIANT</span><span class="p">:</span> <span class="s2">&quot;NMD transcript&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">NON_CODING_TRANSCRIPT_VARIANT</span><span class="p">:</span> <span class="s2">&quot;non-coding transcript&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">UPSTREAM_GENE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;upstream of gene&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">DOWNSTREAM_GENE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;downstream of gene&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">TFBS_ABLATION</span><span class="p">:</span> <span class="s2">&quot;TFBS ablation&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">TFBS_AMPLIFICATION</span><span class="p">:</span> <span class="s2">&quot;TFBS amplification&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">TF_BINDING_SITE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;TFBS binding site&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">REGULATORY_REGION_ABLATION</span><span class="p">:</span> <span class="s2">&quot;regulatory region ablation&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">REGULATORY_REGION_AMPLIFICATION</span><span class="p">:</span> <span class="s2">&quot;regulatory region amplification&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">FEATURE_ELONGATION</span><span class="p">:</span> <span class="s2">&quot;feature elongation&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">REGULATORY_REGION_VARIANT</span><span class="p">:</span> <span class="s2">&quot;regulatory region&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">FEATURE_TRUNCATION</span><span class="p">:</span> <span class="s2">&quot;feature truncation&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INTERGENIC_VARIANT</span><span class="p">:</span> <span class="s2">&quot;intergenic&quot;</span><span class="p">,</span>
+    <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SEQUENCE_VARIANT</span><span class="p">:</span> <span class="s2">&quot;sequence variant&quot;</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="n">so_id_to_display</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;SO:1000029&quot;</span><span class="p">:</span> <span class="s2">&quot;chromosomal deletion&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;SO:1000037&quot;</span><span class="p">:</span> <span class="s2">&quot;chromosomal duplication&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;SO:1000030&quot;</span><span class="p">:</span> <span class="s2">&quot;chromosomal_inversion&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;SO:1000044&quot;</span><span class="p">:</span> <span class="s2">&quot;chromosomal_translocation&quot;</span><span class="p">,</span>
+<span class="p">}</span>
 </pre></div>
 
            </div>
diff --git a/stable/_modules/gpsea/model/genome/_genome.html b/stable/_modules/gpsea/model/genome/_genome.html
index 3c46ddc00..ef76cd591 100644
--- a/stable/_modules/gpsea/model/genome/_genome.html
+++ b/stable/_modules/gpsea/model/genome/_genome.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model.genome._genome &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model.genome._genome &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_api.html b/stable/_modules/gpsea/preprocessing/_api.html
index 56b8c8db7..652dc4e63 100644
--- a/stable/_modules/gpsea/preprocessing/_api.html
+++ b/stable/_modules/gpsea/preprocessing/_api.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._api &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._api &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_audit.html b/stable/_modules/gpsea/preprocessing/_audit.html
index ddf27eb06..6207b226f 100644
--- a/stable/_modules/gpsea/preprocessing/_audit.html
+++ b/stable/_modules/gpsea/preprocessing/_audit.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._audit &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._audit &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_config.html b/stable/_modules/gpsea/preprocessing/_config.html
index 6752986b6..c2b2bd1cb 100644
--- a/stable/_modules/gpsea/preprocessing/_config.html
+++ b/stable/_modules/gpsea/preprocessing/_config.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._config &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._config &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
@@ -564,7 +564,7 @@ <h1>Source code for gpsea.preprocessing._config</h1><div class="highlight"><pre>
     <span class="c1"># Turn phenopackets into a cohort using the cohort creator.</span>
     <span class="c1"># Keep track of the progress by wrapping the list of phenopackets</span>
     <span class="c1"># with TQDM 😎</span>
-    <span class="n">cohort_iter</span> <span class="o">=</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Patients Created&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
+    <span class="n">cohort_iter</span> <span class="o">=</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Individuals Processed&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="n">unit</span><span class="o">=</span><span class="s2">&quot;individuals&quot;</span><span class="p">)</span>
     <span class="n">notepad</span> <span class="o">=</span> <span class="n">cohort_creator</span><span class="o">.</span><span class="n">prepare_notepad</span><span class="p">(</span><span class="s2">&quot;Phenopackets&quot;</span><span class="p">)</span>
     <span class="n">cohort</span> <span class="o">=</span> <span class="n">cohort_creator</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">cohort_iter</span><span class="p">,</span> <span class="n">notepad</span><span class="p">)</span>
 
diff --git a/stable/_modules/gpsea/preprocessing/_generic.html b/stable/_modules/gpsea/preprocessing/_generic.html
index 4ee6269e0..4312363e8 100644
--- a/stable/_modules/gpsea/preprocessing/_generic.html
+++ b/stable/_modules/gpsea/preprocessing/_generic.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._generic &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._generic &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_patient.html b/stable/_modules/gpsea/preprocessing/_patient.html
index 1074aa541..a061987cc 100644
--- a/stable/_modules/gpsea/preprocessing/_patient.html
+++ b/stable/_modules/gpsea/preprocessing/_patient.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._patient &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._patient &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_phenopacket.html b/stable/_modules/gpsea/preprocessing/_phenopacket.html
index 8539a70b9..9d90f46f5 100644
--- a/stable/_modules/gpsea/preprocessing/_phenopacket.html
+++ b/stable/_modules/gpsea/preprocessing/_phenopacket.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._phenopacket &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._phenopacket &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_phenotype.html b/stable/_modules/gpsea/preprocessing/_phenotype.html
index bd0b84194..573888b06 100644
--- a/stable/_modules/gpsea/preprocessing/_phenotype.html
+++ b/stable/_modules/gpsea/preprocessing/_phenotype.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._phenotype &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._phenotype &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_protein.html b/stable/_modules/gpsea/preprocessing/_protein.html
index de2a1705c..791ede2da 100644
--- a/stable/_modules/gpsea/preprocessing/_protein.html
+++ b/stable/_modules/gpsea/preprocessing/_protein.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._protein &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._protein &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_uniprot.html b/stable/_modules/gpsea/preprocessing/_uniprot.html
index 12117f710..cef1e64b6 100644
--- a/stable/_modules/gpsea/preprocessing/_uniprot.html
+++ b/stable/_modules/gpsea/preprocessing/_uniprot.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._uniprot &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._uniprot &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
@@ -95,10 +95,8 @@ <h1>Source code for gpsea.preprocessing._uniprot</h1><div class="highlight"><pre
 <a class="viewcode-back" href="../../../apidocs/gpsea.preprocessing.html#gpsea.preprocessing.UniprotProteinMetadataService">[docs]</a>
 <span class="k">class</span> <span class="nc">UniprotProteinMetadataService</span><span class="p">(</span><span class="n">ProteinMetadataService</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;A class that creates ProteinMetadata objects from data found with the Uniprot REST API.</span>
-<span class="sd">    More info on the Uniprot REST API here - https://www.uniprot.org/help/programmatic_access</span>
-
-<span class="sd">    Methods:</span>
-<span class="sd">        annotate(protein_id:str): Gets metadata and creates ProteinMetadata for given protein ID</span>
+<span class="sd">    More info on the Uniprot REST API are</span>
+<span class="sd">    in the `Programmatic access &lt;https://www.uniprot.org/help/programmatic_access&gt;`_ section.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
@@ -114,8 +112,8 @@ <h1>Source code for gpsea.preprocessing._uniprot</h1><div class="highlight"><pre
 <a class="viewcode-back" href="../../../apidocs/gpsea.preprocessing.html#gpsea.preprocessing.UniprotProteinMetadataService.parse_uniprot_json">[docs]</a>
     <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">parse_uniprot_json</span><span class="p">(</span>
-            <span class="n">payload</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Mapping</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">typing</span><span class="o">.</span><span class="n">Any</span><span class="p">],</span>
-            <span class="n">protein_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">payload</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Mapping</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">typing</span><span class="o">.</span><span class="n">Any</span><span class="p">],</span>
+        <span class="n">protein_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">ProteinMetadata</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Try to extract `ProteinMetadata` corresponding to `protein_id` from the Uniprot JSON `payload`.</span>
@@ -131,41 +129,54 @@ <h1>Source code for gpsea.preprocessing._uniprot</h1><div class="highlight"><pre
         <span class="n">results</span> <span class="o">=</span> <span class="n">payload</span><span class="p">[</span><span class="s1">&#39;results&#39;</span><span class="p">]</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">results</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;No proteins found for ID </span><span class="si">{</span><span class="n">protein_id</span><span class="si">}</span><span class="s2">. Please verify refseq ID.&quot;</span><span class="p">)</span>
-
-        <span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">results</span><span class="p">:</span>
-            <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">uni</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="n">protein_id</span> <span class="k">for</span> <span class="n">uni</span> <span class="ow">in</span> <span class="n">protein</span><span class="p">[</span><span class="s1">&#39;uniProtKBCrossReferences&#39;</span><span class="p">]):</span>
-                <span class="c1"># `protein` has a cross-reference to the `protein_id` of interest</span>
-                <span class="k">try</span><span class="p">:</span>
-                    <span class="n">protein_name</span> <span class="o">=</span> <span class="n">protein</span><span class="p">[</span><span class="s1">&#39;proteinDescription&#39;</span><span class="p">][</span><span class="s1">&#39;recommendedName&#39;</span><span class="p">][</span><span class="s1">&#39;fullName&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">]</span>
-                <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
-                    <span class="n">protein_name</span> <span class="o">=</span> <span class="n">protein</span><span class="p">[</span><span class="s1">&#39;proteinDescription&#39;</span><span class="p">][</span><span class="s1">&#39;submissionNames&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s1">&#39;fullName&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">]</span>
-
-                <span class="n">all_features_list</span> <span class="o">=</span> <span class="p">[]</span>
-                <span class="k">try</span><span class="p">:</span>
-                    <span class="k">for</span> <span class="n">feature</span> <span class="ow">in</span> <span class="n">protein</span><span class="p">[</span><span class="s1">&#39;features&#39;</span><span class="p">]:</span>
-                        <span class="n">feature_start</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">feature</span><span class="p">[</span><span class="s1">&#39;location&#39;</span><span class="p">][</span><span class="s1">&#39;start&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">])</span>
-                        <span class="n">feature_end</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">feature</span><span class="p">[</span><span class="s1">&#39;location&#39;</span><span class="p">][</span><span class="s1">&#39;end&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">])</span>
-                        <span class="n">feature_name</span> <span class="o">=</span> <span class="n">feature</span><span class="p">[</span><span class="s1">&#39;description&#39;</span><span class="p">]</span>
-                        <span class="n">feature_info</span> <span class="o">=</span> <span class="n">FeatureInfo</span><span class="p">(</span>
-                            <span class="n">feature_name</span><span class="p">,</span>
-                            <span class="n">Region</span><span class="p">(</span><span class="n">start</span><span class="o">=</span><span class="n">feature_start</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="n">feature_end</span><span class="p">),</span>
-                        <span class="p">)</span>
-                        <span class="n">feature_type</span> <span class="o">=</span> <span class="n">FeatureType</span><span class="p">[</span><span class="n">feature</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()]</span>
-                        <span class="n">protein_feature</span> <span class="o">=</span> <span class="n">ProteinFeature</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">feature_info</span><span class="p">,</span> <span class="n">feature_type</span><span class="p">)</span>
-                        <span class="n">all_features_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">protein_feature</span><span class="p">)</span>
-                <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
-                    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;No features for </span><span class="si">{</span><span class="n">protein_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-
-                <span class="k">try</span><span class="p">:</span>
-                    <span class="n">protein_length</span> <span class="o">=</span> <span class="n">protein</span><span class="p">[</span><span class="s2">&quot;sequence&quot;</span><span class="p">][</span><span class="s2">&quot;length&quot;</span><span class="p">]</span>
-                <span class="k">except</span> <span class="ne">KeyError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
-                    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
-
-                <span class="k">return</span> <span class="n">ProteinMetadata</span><span class="p">(</span><span class="n">protein_id</span><span class="p">,</span> <span class="n">protein_name</span><span class="p">,</span> <span class="n">all_features_list</span><span class="p">,</span> <span class="n">protein_length</span><span class="p">)</span>
+        <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">results</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="c1"># In case we get only one result, let&#39;s use it!</span>
+            <span class="k">return</span> <span class="n">UniprotProteinMetadataService</span><span class="o">.</span><span class="n">_extract_metadata</span><span class="p">(</span>
+                <span class="n">protein_id</span><span class="o">=</span><span class="n">protein_id</span><span class="p">,</span>
+                <span class="n">data</span><span class="o">=</span><span class="n">results</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">results</span><span class="p">:</span>
+                <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">uni</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="n">protein_id</span> <span class="k">for</span> <span class="n">uni</span> <span class="ow">in</span> <span class="n">protein</span><span class="p">[</span><span class="s1">&#39;uniProtKBCrossReferences&#39;</span><span class="p">]):</span>
+                    <span class="k">return</span> <span class="n">UniprotProteinMetadataService</span><span class="o">.</span><span class="n">_extract_metadata</span><span class="p">(</span>
+                        <span class="n">protein_id</span><span class="o">=</span><span class="n">protein_id</span><span class="p">,</span>
+                        <span class="n">data</span><span class="o">=</span><span class="n">protein</span><span class="p">,</span>
+                    <span class="p">)</span>
 
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Could not find an entry for </span><span class="si">{</span><span class="n">protein_id</span><span class="si">}</span><span class="s1"> in Uniprot response&#39;</span><span class="p">)</span></div>
 
 
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_extract_metadata</span><span class="p">(</span><span class="n">protein_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Mapping</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">typing</span><span class="o">.</span><span class="n">Any</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">ProteinMetadata</span><span class="p">:</span>
+        <span class="c1"># `protein` has a cross-reference to the `protein_id` of interest</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">protein_name</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;proteinDescription&#39;</span><span class="p">][</span><span class="s1">&#39;recommendedName&#39;</span><span class="p">][</span><span class="s1">&#39;fullName&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">]</span>
+        <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+            <span class="n">protein_name</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;proteinDescription&#39;</span><span class="p">][</span><span class="s1">&#39;submissionNames&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s1">&#39;fullName&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">]</span>
+
+        <span class="n">all_features_list</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">feature</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;features&#39;</span><span class="p">]:</span>
+                <span class="n">feature_start</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">feature</span><span class="p">[</span><span class="s1">&#39;location&#39;</span><span class="p">][</span><span class="s1">&#39;start&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">])</span>
+                <span class="n">feature_end</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">feature</span><span class="p">[</span><span class="s1">&#39;location&#39;</span><span class="p">][</span><span class="s1">&#39;end&#39;</span><span class="p">][</span><span class="s1">&#39;value&#39;</span><span class="p">])</span>
+                <span class="n">feature_name</span> <span class="o">=</span> <span class="n">feature</span><span class="p">[</span><span class="s1">&#39;description&#39;</span><span class="p">]</span>
+                <span class="n">feature_info</span> <span class="o">=</span> <span class="n">FeatureInfo</span><span class="p">(</span>
+                    <span class="n">feature_name</span><span class="p">,</span>
+                    <span class="n">Region</span><span class="p">(</span><span class="n">start</span><span class="o">=</span><span class="n">feature_start</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="n">feature_end</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="n">feature_type</span> <span class="o">=</span> <span class="n">FeatureType</span><span class="p">[</span><span class="n">feature</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()]</span>
+                <span class="n">protein_feature</span> <span class="o">=</span> <span class="n">ProteinFeature</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">feature_info</span><span class="p">,</span> <span class="n">feature_type</span><span class="p">)</span>
+                <span class="n">all_features_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">protein_feature</span><span class="p">)</span>
+        <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;No features for </span><span class="si">{</span><span class="n">protein_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">protein_length</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;sequence&quot;</span><span class="p">][</span><span class="s2">&quot;length&quot;</span><span class="p">]</span>
+        <span class="k">except</span> <span class="ne">KeyError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">ProteinMetadata</span><span class="p">(</span><span class="n">protein_id</span><span class="p">,</span> <span class="n">protein_name</span><span class="p">,</span> <span class="n">all_features_list</span><span class="p">,</span> <span class="n">protein_length</span><span class="p">)</span>
+
 <div class="viewcode-block" id="UniprotProteinMetadataService.annotate">
 <a class="viewcode-back" href="../../../apidocs/gpsea.preprocessing.html#gpsea.preprocessing.UniprotProteinMetadataService.annotate">[docs]</a>
     <span class="k">def</span> <span class="nf">annotate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">ProteinMetadata</span><span class="p">:</span>
@@ -186,6 +197,7 @@ <h1>Source code for gpsea.preprocessing._uniprot</h1><div class="highlight"><pre
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;only works with a RefSeq database ID (e.g. NP_037407.4), but we got </span><span class="si">{</span><span class="n">protein_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="n">api_url</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_url</span> <span class="o">%</span> <span class="n">protein_id</span>
         <span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_timeout</span><span class="p">)</span><span class="o">.</span><span class="n">json</span><span class="p">()</span>
+
         <span class="k">return</span> <span class="n">UniprotProteinMetadataService</span><span class="o">.</span><span class="n">parse_uniprot_json</span><span class="p">(</span><span class="n">response</span><span class="p">,</span> <span class="n">protein_id</span><span class="p">)</span></div>
 </div>
 
diff --git a/stable/_modules/gpsea/preprocessing/_variant.html b/stable/_modules/gpsea/preprocessing/_variant.html
index 971eedb6c..5cc48495c 100644
--- a/stable/_modules/gpsea/preprocessing/_variant.html
+++ b/stable/_modules/gpsea/preprocessing/_variant.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._variant &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._variant &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_vep.html b/stable/_modules/gpsea/preprocessing/_vep.html
index 50b490e55..576fe9661 100644
--- a/stable/_modules/gpsea/preprocessing/_vep.html
+++ b/stable/_modules/gpsea/preprocessing/_vep.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._vep &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._vep &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/preprocessing/_vv.html b/stable/_modules/gpsea/preprocessing/_vv.html
index ea0132490..04e448a5e 100644
--- a/stable/_modules/gpsea/preprocessing/_vv.html
+++ b/stable/_modules/gpsea/preprocessing/_vv.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing._vv &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing._vv &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/view/_cohort.html b/stable/_modules/gpsea/view/_cohort.html
index cde6f515c..a9dcd4bc0 100644
--- a/stable/_modules/gpsea/view/_cohort.html
+++ b/stable/_modules/gpsea/view/_cohort.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._cohort &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._cohort &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/view/_cohort_variant_viewer.html b/stable/_modules/gpsea/view/_cohort_variant_viewer.html
new file mode 100644
index 000000000..dbd394d1c
--- /dev/null
+++ b/stable/_modules/gpsea/view/_cohort_variant_viewer.html
@@ -0,0 +1,277 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>gpsea.view._cohort_variant_viewer &mdash; GPSEA 0.4.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/gpsea.css?v=547657ed" />
+
+  
+  <!--[if lt IE 9]>
+    <script src="../../../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="../../../_static/copybutton.js?v=6dbb43f8"></script>
+    <script src="../../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../../genindex.html" />
+    <link rel="search" title="Search" href="../../../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../../../index.html" class="icon icon-home">
+            GPSEA
+          </a>
+              <div class="version">
+                0.4
+              </div>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Installation &amp; Tutorial</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../tutorial.html">Tutorial</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../user-guide/index.html">User guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../apidocs/modules.html">API reference</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../../../index.html">GPSEA</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">gpsea.view._cohort_variant_viewer</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <h1>Source code for gpsea.view._cohort_variant_viewer</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">typing</span>
+
+<span class="kn">from</span> <span class="nn">jinja2</span> <span class="kn">import</span> <span class="n">Environment</span><span class="p">,</span> <span class="n">PackageLoader</span>
+<span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">namedtuple</span><span class="p">,</span> <span class="n">defaultdict</span>
+
+<span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">Cohort</span><span class="p">,</span> <span class="n">Variant</span><span class="p">,</span> <span class="n">VariantEffect</span>
+<span class="kn">from</span> <span class="nn">._formatter</span> <span class="kn">import</span> <span class="n">VariantFormatter</span>
+
+
+<span class="n">ToDisplay</span> <span class="o">=</span> <span class="n">namedtuple</span><span class="p">(</span><span class="s1">&#39;ToDisplay&#39;</span><span class="p">,</span> <span class="p">[</span><span class="s1">&#39;hgvs_cdna&#39;</span><span class="p">,</span> <span class="s1">&#39;hgvsp&#39;</span><span class="p">,</span> <span class="s1">&#39;variant_effects&#39;</span><span class="p">])</span>
+
+<span class="n">VariantData</span> <span class="o">=</span> <span class="n">namedtuple</span><span class="p">(</span><span class="s1">&#39;VariantData&#39;</span><span class="p">,</span> <span class="p">[</span><span class="s1">&#39;variant_key&#39;</span><span class="p">,</span> <span class="s1">&#39;hgvs_cdna&#39;</span><span class="p">,</span> <span class="s1">&#39;hgvsp&#39;</span><span class="p">,</span> <span class="s1">&#39;variant_effects&#39;</span><span class="p">])</span>
+
+
+<div class="viewcode-block" id="CohortVariantViewer">
+<a class="viewcode-back" href="../../../apidocs/gpsea.view.html#gpsea.view.CohortVariantViewer">[docs]</a>
+<span class="k">class</span> <span class="nc">CohortVariantViewer</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    `CohortVariantViewer` creates an HTML report with the cohort variants.</span>
+
+<span class="sd">    The report can be either written into an HTML file or displayed in a Jupyter notebook.</span>
+
+<span class="sd">    See :ref:show-cohort-variants: for an example usage.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">tx_id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args:</span>
+<span class="sd">            tx_id (str): The transcript identifier (Usually, the MANE RefSeq transcript, that should start with &quot;NM_&quot;)</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">environment</span> <span class="o">=</span> <span class="n">Environment</span><span class="p">(</span><span class="n">loader</span><span class="o">=</span><span class="n">PackageLoader</span><span class="p">(</span><span class="s1">&#39;gpsea.view&#39;</span><span class="p">,</span> <span class="s1">&#39;templates&#39;</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_cohort_template</span> <span class="o">=</span> <span class="n">environment</span><span class="o">.</span><span class="n">get_template</span><span class="p">(</span><span class="s2">&quot;all_variants.html&quot;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_var_formatter</span> <span class="o">=</span> <span class="n">VariantFormatter</span><span class="p">(</span><span class="n">tx_id</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">tx_id</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;NM&quot;</span><span class="p">):</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;[WARNING] Non-RefSeq transcript id: </span><span class="si">{</span><span class="n">tx_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_transcript_id</span> <span class="o">=</span> <span class="n">tx_id</span>
+
+<div class="viewcode-block" id="CohortVariantViewer.process">
+<a class="viewcode-back" href="../../../apidocs/gpsea.view.html#gpsea.view.CohortVariantViewer.process">[docs]</a>
+    <span class="k">def</span> <span class="nf">process</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">cohort</span><span class="p">:</span> <span class="n">Cohort</span><span class="p">,</span>
+        <span class="n">only_hgvs</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Create an HTML that should be shown with ``display(HTML(..))`` of the ipython package.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            cohort (Cohort): The cohort being analyzed in the current notebook.</span>
+<span class="sd">            only_hgvs (bool): Do not show the transcript ID part of the HGVS annotation, just the annotation.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            str: an HTML string with parameterized template for rendering</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">context</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_prepare_context</span><span class="p">(</span><span class="n">cohort</span><span class="p">,</span> <span class="n">only_hgvs</span><span class="o">=</span><span class="n">only_hgvs</span><span class="p">)</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cohort_template</span><span class="o">.</span><span class="n">render</span><span class="p">(</span><span class="n">context</span><span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">_prepare_context</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">cohort</span><span class="p">:</span> <span class="n">Cohort</span><span class="p">,</span>
+        <span class="n">only_hgvs</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Mapping</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">typing</span><span class="o">.</span><span class="n">Any</span><span class="p">]:</span>
+        <span class="n">variant_count_dictionary</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
+        <span class="n">variant_effect_count_dictionary</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
+        <span class="n">variant_key_to_variant</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="n">cohort</span><span class="o">.</span><span class="n">all_variants</span><span class="p">():</span>
+            <span class="n">var_key</span> <span class="o">=</span> <span class="n">var</span><span class="o">.</span><span class="n">variant_info</span><span class="o">.</span><span class="n">variant_key</span>
+            <span class="n">vdata</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_variant_data</span><span class="p">(</span><span class="n">var</span><span class="p">,</span> <span class="n">only_hgvs</span><span class="p">)</span>
+            <span class="n">variant_key_to_variant</span><span class="p">[</span><span class="n">var_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">vdata</span>
+            <span class="n">variant_count_dictionary</span><span class="p">[</span><span class="n">var_key</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+            <span class="k">for</span> <span class="n">v_eff</span> <span class="ow">in</span> <span class="n">vdata</span><span class="o">.</span><span class="n">variant_effects</span><span class="p">:</span>
+                <span class="n">variant_effect_count_dictionary</span><span class="p">[</span><span class="n">v_eff</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+        <span class="n">variant_counts</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+        <span class="n">variant_effect_counts</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">var_key</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">variant_count_dictionary</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="n">var_data</span> <span class="o">=</span> <span class="n">variant_key_to_variant</span><span class="p">[</span><span class="n">var_key</span><span class="p">]</span>
+            <span class="n">variant_counts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="p">{</span>
+                    <span class="s2">&quot;variant_key&quot;</span><span class="p">:</span> <span class="n">var_data</span><span class="o">.</span><span class="n">variant_key</span><span class="p">,</span>
+                    <span class="s2">&quot;variant&quot;</span><span class="p">:</span> <span class="n">var_data</span><span class="o">.</span><span class="n">hgvs_cdna</span><span class="p">,</span>
+                    <span class="s2">&quot;variant_name&quot;</span><span class="p">:</span> <span class="n">var_data</span><span class="o">.</span><span class="n">hgvs_cdna</span><span class="p">,</span>
+                    <span class="s2">&quot;protein_name&quot;</span><span class="p">:</span> <span class="n">var_data</span><span class="o">.</span><span class="n">hgvsp</span><span class="p">,</span>
+                    <span class="s2">&quot;variant_effects&quot;</span><span class="p">:</span> <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">var_data</span><span class="o">.</span><span class="n">variant_effects</span><span class="p">),</span>
+                    <span class="s2">&quot;count&quot;</span><span class="p">:</span> <span class="n">count</span><span class="p">,</span>
+                <span class="p">}</span>
+            <span class="p">)</span>
+        <span class="k">for</span> <span class="n">v_effect</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">variant_effect_count_dictionary</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="n">variant_effect_counts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="p">{</span>
+                    <span class="s2">&quot;effect&quot;</span><span class="p">:</span> <span class="n">v_effect</span><span class="p">,</span>
+                    <span class="s2">&quot;count&quot;</span><span class="p">:</span> <span class="n">count</span>
+                <span class="p">}</span>
+            <span class="p">)</span>
+        <span class="n">variant_counts</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">variant_counts</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">row</span><span class="p">:</span> <span class="n">row</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;count&quot;</span><span class="p">),</span> <span class="n">reverse</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">variant_effect_counts</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">variant_effect_counts</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">row</span><span class="p">:</span> <span class="n">row</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;count&quot;</span><span class="p">),</span> <span class="n">reverse</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+        <span class="c1"># The following dictionary is used by the Jinja2 HTML template</span>
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="s2">&quot;has_transcript&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;variant_count_list&quot;</span><span class="p">:</span> <span class="n">variant_counts</span><span class="p">,</span>
+            <span class="s2">&quot;variant_effect_count_list&quot;</span><span class="p">:</span> <span class="n">variant_effect_counts</span><span class="p">,</span>
+            <span class="s2">&quot;total_unique_allele_count&quot;</span><span class="p">:</span> <span class="nb">len</span><span class="p">(</span><span class="n">variant_counts</span><span class="p">)</span>
+        <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">_get_variant_data</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">variant</span><span class="p">:</span> <span class="n">Variant</span><span class="p">,</span>
+        <span class="n">only_hgvs</span><span class="p">:</span> <span class="nb">bool</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">VariantData</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Get user-friendly strings (e.g., HGVS for our target transcript) to match to the chromosomal strings</span>
+<span class="sd">        Args:</span>
+<span class="sd">            variant (Variant): The variant to be formatted.</span>
+<span class="sd">            only_hgvs (bool): do not show the transcript ID part of the HGVS annotation, just the annotation.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            VariantData: a named tuple with variant data formatted for human consumption.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">variant_key</span> <span class="o">=</span> <span class="n">variant</span><span class="o">.</span><span class="n">variant_info</span><span class="o">.</span><span class="n">variant_key</span>
+        <span class="k">if</span> <span class="n">variant</span><span class="o">.</span><span class="n">variant_info</span><span class="o">.</span><span class="n">has_sv_info</span><span class="p">():</span>
+            <span class="n">sv_info</span> <span class="o">=</span> <span class="n">variant</span><span class="o">.</span><span class="n">variant_info</span><span class="o">.</span><span class="n">sv_info</span>
+            <span class="n">gene_symbol</span> <span class="o">=</span> <span class="n">sv_info</span><span class="o">.</span><span class="n">gene_symbol</span>
+            <span class="n">display</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SV involving </span><span class="si">{</span><span class="n">gene_symbol</span><span class="si">}</span><span class="s2">&quot;</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">structural_so_id_to_display</span><span class="p">(</span><span class="n">so_term</span><span class="o">=</span><span class="n">sv_info</span><span class="o">.</span><span class="n">structural_type</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">VariantData</span><span class="p">(</span>
+                <span class="n">variant_key</span><span class="o">=</span><span class="n">variant_key</span><span class="p">,</span>
+                <span class="n">hgvs_cdna</span><span class="o">=</span><span class="n">display</span><span class="p">,</span>
+                <span class="n">hgvsp</span><span class="o">=</span><span class="s2">&quot;p.?&quot;</span><span class="p">,</span>
+                <span class="n">variant_effects</span><span class="o">=</span><span class="p">[</span><span class="n">effect</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">variant_key</span> <span class="o">=</span> <span class="n">variant</span><span class="o">.</span><span class="n">variant_info</span><span class="o">.</span><span class="n">variant_key</span>
+            <span class="n">display</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_var_formatter</span><span class="o">.</span><span class="n">format_as_string</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+            <span class="n">tx_annotation</span> <span class="o">=</span> <span class="n">variant</span><span class="o">.</span><span class="n">get_tx_anno_by_tx_id</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_transcript_id</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">tx_annotation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">hgvsp</span> <span class="o">=</span> <span class="n">tx_annotation</span><span class="o">.</span><span class="n">hgvsp</span>
+                <span class="n">var_effects</span> <span class="o">=</span> <span class="p">[</span><span class="n">var_eff</span><span class="o">.</span><span class="n">to_display</span><span class="p">()</span> <span class="k">for</span> <span class="n">var_eff</span> <span class="ow">in</span> <span class="n">tx_annotation</span><span class="o">.</span><span class="n">variant_effects</span><span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">hgvsp</span> <span class="o">=</span> <span class="kc">None</span>
+                <span class="n">var_effects</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="k">if</span> <span class="n">only_hgvs</span><span class="p">:</span>
+                <span class="c1"># do not show the transcript id</span>
+                <span class="n">fields_dna</span> <span class="o">=</span> <span class="n">display</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;:&quot;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fields_dna</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                    <span class="n">display_hgvs_cDNA</span> <span class="o">=</span> <span class="n">fields_dna</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">display_hgvs_cDNA</span> <span class="o">=</span> <span class="n">fields_dna</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                
+                <span class="n">fields_ps</span> <span class="o">=</span> <span class="n">hgvsp</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;:&quot;</span><span class="p">)</span> <span class="k">if</span> <span class="n">hgvsp</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fields_ps</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                    <span class="n">hgvsp</span> <span class="o">=</span> <span class="n">fields_ps</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">hgvsp</span> <span class="o">=</span> <span class="n">fields_ps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="k">return</span> <span class="n">VariantData</span><span class="p">(</span>
+                <span class="n">variant_key</span><span class="o">=</span><span class="n">variant_key</span><span class="p">,</span>
+                <span class="n">hgvs_cdna</span><span class="o">=</span><span class="n">display_hgvs_cDNA</span><span class="p">,</span>
+                <span class="n">hgvsp</span><span class="o">=</span><span class="n">hgvsp</span><span class="p">,</span>
+                <span class="n">variant_effects</span><span class="o">=</span><span class="n">var_effects</span><span class="p">,</span>
+            <span class="p">)</span></div>
+
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
\ No newline at end of file
diff --git a/stable/_modules/gpsea/view/_disease.html b/stable/_modules/gpsea/view/_disease.html
index 2eb659000..2eff08cd4 100644
--- a/stable/_modules/gpsea/view/_disease.html
+++ b/stable/_modules/gpsea/view/_disease.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._disease &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._disease &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/view/_formatter.html b/stable/_modules/gpsea/view/_formatter.html
index 43e0bd912..cc1ec374c 100644
--- a/stable/_modules/gpsea/view/_formatter.html
+++ b/stable/_modules/gpsea/view/_formatter.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._formatter &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._formatter &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
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diff --git a/stable/_modules/gpsea/view/_phenotype_analysis.html b/stable/_modules/gpsea/view/_phenotype_analysis.html
new file mode 100644
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+             
+  <h1>Source code for gpsea.view._phenotype_analysis</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">hpotk</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">from</span> <span class="nn">gpsea.analysis.pcats</span> <span class="kn">import</span> <span class="n">HpoTermAnalysisResult</span>
+
+
+<div class="viewcode-block" id="summarize_hpo_analysis">
+<a class="viewcode-back" href="../../../apidocs/gpsea.view.html#gpsea.view.summarize_hpo_analysis">[docs]</a>
+<span class="k">def</span> <span class="nf">summarize_hpo_analysis</span><span class="p">(</span>
+    <span class="n">hpo</span><span class="p">:</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">MinimalOntology</span><span class="p">,</span>
+    <span class="n">result</span><span class="p">:</span> <span class="n">HpoTermAnalysisResult</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Create a dataframe with counts, frequencies, and p values for the tested HPO terms.</span>
+
+<span class="sd">    The HPO terms that were not tested will *not* be included in the frame.</span>
+
+<span class="sd">    :param hpo: HPO data.</span>
+<span class="sd">    :param result: the HPO term analysis results to show.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">HpoTermAnalysisResult</span><span class="p">)</span>
+
+    <span class="c1"># Row index: a list of tested HPO terms</span>
+    <span class="n">pheno_idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span>
+    <span class="c1"># Column index: multiindex of counts and percentages for all genotype predicate groups</span>
+    <span class="n">gt_idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_product</span><span class="p">(</span>
+        <span class="n">iterables</span><span class="o">=</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">get_categories</span><span class="p">(),</span> <span class="p">(</span><span class="s2">&quot;Count&quot;</span><span class="p">,</span> <span class="s2">&quot;Percent&quot;</span><span class="p">)),</span>
+        <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">get_question_base</span><span class="p">(),</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="c1"># We&#39;ll fill this frame with data</span>
+    <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">index</span><span class="o">=</span><span class="n">pheno_idx</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="n">gt_idx</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ph_predicate</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">pheno_predicates</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">all_counts</span><span class="p">):</span>
+        <span class="c1"># Sum across the phenotype categories (collapse the rows).</span>
+        <span class="n">gt_totals</span> <span class="o">=</span> <span class="n">count</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">gt_cat</span> <span class="ow">in</span> <span class="n">count</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+            <span class="n">cnt</span> <span class="o">=</span> <span class="n">count</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">ph_predicate</span><span class="o">.</span><span class="n">present_phenotype_category</span><span class="p">,</span> <span class="n">gt_cat</span><span class="p">]</span>
+            <span class="n">total</span> <span class="o">=</span> <span class="n">gt_totals</span><span class="p">[</span><span class="n">gt_cat</span><span class="p">]</span>
+            <span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">ph_predicate</span><span class="o">.</span><span class="n">phenotype</span><span class="p">,</span> <span class="p">(</span><span class="n">gt_cat</span><span class="p">,</span> <span class="s2">&quot;Count&quot;</span><span class="p">)]</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">cnt</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">&quot;</span>
+            <span class="n">pct</span> <span class="o">=</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">total</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="nb">round</span><span class="p">(</span><span class="n">cnt</span> <span class="o">*</span> <span class="mi">100</span> <span class="o">/</span> <span class="n">total</span><span class="p">)</span>
+            <span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">ph_predicate</span><span class="o">.</span><span class="n">phenotype</span><span class="p">,</span> <span class="p">(</span><span class="n">gt_cat</span><span class="p">,</span> <span class="s2">&quot;Percent&quot;</span><span class="p">)]</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">pct</span><span class="si">}</span><span class="s2">%&quot;</span>
+
+    <span class="c1"># Add columns with p values and corrected p values (if present)</span>
+    <span class="n">p_val_col_name</span> <span class="o">=</span> <span class="s2">&quot;p values&quot;</span>
+    <span class="n">corrected_p_val_col_name</span> <span class="o">=</span> <span class="s2">&quot;Corrected p values&quot;</span>
+    <span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">corrected_pvals</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">df</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">corrected_p_val_col_name</span><span class="p">),</span> <span class="n">result</span><span class="o">.</span><span class="n">corrected_pvals</span><span class="p">)</span>
+    <span class="n">df</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">),</span> <span class="n">result</span><span class="o">.</span><span class="n">pvals</span><span class="p">)</span>
+
+    <span class="c1"># Format the index values: `HP:0001250` -&gt; `Seizure [HP:0001250]` if the index members are HPO terms</span>
+    <span class="c1"># or just use the term ID CURIE otherwise (e.g. `OMIM:123000`).</span>
+    <span class="n">labeled_idx</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">term_id</span><span class="p">:</span> <span class="n">format_term_id</span><span class="p">(</span><span class="n">hpo</span><span class="p">,</span> <span class="n">term_id</span><span class="p">))</span>
+
+    <span class="c1"># Last, sort by corrected p value or just p value</span>
+    <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="n">labeled_idx</span><span class="p">)</span>
+    <span class="c1"># and only report the tested HPO terms</span>
+    <span class="n">with_p_value</span> <span class="o">=</span> <span class="n">df</span><span class="p">[(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">)]</span><span class="o">.</span><span class="n">notna</span><span class="p">()</span>
+    <span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">corrected_pvals</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">corrected_p_val_col_name</span><span class="p">),</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">)])</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">with_p_value</span><span class="p">]</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">p_val_col_name</span><span class="p">))</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">with_p_value</span><span class="p">]</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">format_term_id</span><span class="p">(</span>
+    <span class="n">hpo</span><span class="p">:</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">MinimalOntology</span><span class="p">,</span>
+    <span class="n">term_id</span><span class="p">:</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Format a `term_id` as a `str`. HPO term ID is formatted as `&lt;name&gt; [&lt;term_id&gt;]` whereas other term IDs</span>
+<span class="sd">    are formatted as CURIEs (e.g. `OMIM:123000`).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">term_id</span><span class="o">.</span><span class="n">prefix</span> <span class="o">==</span> <span class="s2">&quot;HP&quot;</span><span class="p">:</span>
+        <span class="n">term_name</span> <span class="o">=</span> <span class="n">hpo</span><span class="o">.</span><span class="n">get_term_name</span><span class="p">(</span><span class="n">term_id</span><span class="p">)</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">term_name</span><span class="si">}</span><span class="s2"> [</span><span class="si">{</span><span class="n">term_id</span><span class="o">.</span><span class="n">value</span><span class="si">}</span><span class="s2">]&quot;</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">term_id</span><span class="o">.</span><span class="n">value</span>
+</pre></div>
+
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diff --git a/stable/_modules/gpsea/view/_protein_viewer.html b/stable/_modules/gpsea/view/_protein_viewer.html
index b8bccec41..2a90dacca 100644
--- a/stable/_modules/gpsea/view/_protein_viewer.html
+++ b/stable/_modules/gpsea/view/_protein_viewer.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._protein_viewer &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._protein_viewer &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -38,7 +38,7 @@
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           </a>
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-                0.3
+                0.4
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 <div role="search">
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diff --git a/stable/_modules/gpsea/view/_protein_visualizable.html b/stable/_modules/gpsea/view/_protein_visualizable.html
index 6e394b2cc..d84de66fd 100644
--- a/stable/_modules/gpsea/view/_protein_visualizable.html
+++ b/stable/_modules/gpsea/view/_protein_visualizable.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._protein_visualizable &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._protein_visualizable &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
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         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
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         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -38,7 +38,7 @@
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           </a>
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-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/view/_protein_visualizer.html b/stable/_modules/gpsea/view/_protein_visualizer.html
index b9e887863..a4f38ddce 100644
--- a/stable/_modules/gpsea/view/_protein_visualizer.html
+++ b/stable/_modules/gpsea/view/_protein_visualizer.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._protein_visualizer &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._protein_visualizer &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/gpsea/view/_stats.html b/stable/_modules/gpsea/view/_stats.html
index 6dfc51fa0..45ee0d563 100644
--- a/stable/_modules/gpsea/view/_stats.html
+++ b/stable/_modules/gpsea/view/_stats.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._stats &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._stats &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
@@ -131,12 +131,19 @@ <h1>Source code for gpsea.view._stats</h1><div class="highlight"><pre>
         <span class="n">counts</span> <span class="o">=</span> <span class="n">Counter</span><span class="p">()</span>
         <span class="k">for</span> <span class="n">result</span> <span class="ow">in</span> <span class="n">report</span><span class="o">.</span><span class="n">mtc_filter_results</span><span class="p">:</span>
             <span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">is_filtered_out</span><span class="p">():</span>
-                <span class="n">counts</span><span class="p">[</span><span class="n">result</span><span class="o">.</span><span class="n">reason</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+                <span class="n">counts</span><span class="p">[</span><span class="n">result</span><span class="o">.</span><span class="n">mtc_issue</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
 
         <span class="n">n_skipped</span> <span class="o">=</span> <span class="mi">0</span>
-        <span class="n">reason_to_count</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">reason</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">counts</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">item</span><span class="p">:</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">reverse</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">reason_to_count</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s2">&quot;reason&quot;</span><span class="p">:</span> <span class="n">reason</span><span class="p">,</span> <span class="s2">&quot;count&quot;</span><span class="p">:</span> <span class="n">count</span><span class="p">})</span>
+        <span class="n">issue_to_count</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">mtc_issue</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span>
+            <span class="n">counts</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span>
+            <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">issue2count</span><span class="p">:</span> <span class="p">(</span><span class="n">issue2count</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">code</span><span class="p">,</span> <span class="n">issue2count</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">reason</span><span class="p">)</span>
+        <span class="p">):</span>
+            <span class="n">issue_to_count</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s2">&quot;code&quot;</span><span class="p">:</span> <span class="n">mtc_issue</span><span class="o">.</span><span class="n">code</span><span class="p">,</span>
+                <span class="s2">&quot;reason&quot;</span><span class="p">:</span> <span class="n">mtc_issue</span><span class="o">.</span><span class="n">reason</span><span class="p">,</span>
+                <span class="s2">&quot;count&quot;</span><span class="p">:</span> <span class="n">count</span><span class="p">,</span>
+            <span class="p">})</span>
             <span class="n">n_skipped</span> <span class="o">+=</span> <span class="n">count</span>
 
         <span class="n">n_all</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">report</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span>
@@ -149,7 +156,7 @@ <h1>Source code for gpsea.view._stats</h1><div class="highlight"><pre>
             <span class="s2">&quot;skipped_hpo_count&quot;</span><span class="p">:</span> <span class="n">n_skipped</span><span class="p">,</span>
             <span class="s2">&quot;tested_hpo_count&quot;</span><span class="p">:</span> <span class="n">n_tested</span><span class="p">,</span>
             <span class="s2">&quot;total_hpo_count&quot;</span><span class="p">:</span> <span class="n">n_all</span><span class="p">,</span>
-            <span class="s2">&quot;reason_to_count&quot;</span><span class="p">:</span> <span class="n">reason_to_count</span><span class="p">,</span>
+            <span class="s2">&quot;issue_to_count&quot;</span><span class="p">:</span> <span class="n">issue_to_count</span><span class="p">,</span>
         <span class="p">}</span></div>
 
 </pre></div>
diff --git a/stable/_modules/gpsea/view/_txp.html b/stable/_modules/gpsea/view/_txp.html
index 8901f29c9..c41f21f15 100644
--- a/stable/_modules/gpsea/view/_txp.html
+++ b/stable/_modules/gpsea/view/_txp.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view._txp &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view._txp &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../../../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
diff --git a/stable/_modules/index.html b/stable/_modules/index.html
index 9d7a4f952..80687f9ef 100644
--- a/stable/_modules/index.html
+++ b/stable/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Overview: module code &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -94,7 +94,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="gpsea/analysis/pscore/_impl.html">gpsea.analysis.pscore._impl</a></li>
 <li><a href="gpsea/analysis/pscore/stats/_stats.html">gpsea.analysis.pscore.stats._stats</a></li>
 <li><a href="gpsea/config.html">gpsea.config</a></li>
-<li><a href="gpsea/data/_toy.html">gpsea.data._toy</a></li>
 <li><a href="gpsea/io.html">gpsea.io</a></li>
 <li><a href="gpsea/model/_base.html">gpsea.model._base</a></li>
 <li><a href="gpsea/model/_cohort.html">gpsea.model._cohort</a></li>
@@ -118,8 +117,10 @@ <h1>All modules for which code is available</h1>
 <li><a href="gpsea/preprocessing/_vep.html">gpsea.preprocessing._vep</a></li>
 <li><a href="gpsea/preprocessing/_vv.html">gpsea.preprocessing._vv</a></li>
 <li><a href="gpsea/view/_cohort.html">gpsea.view._cohort</a></li>
+<li><a href="gpsea/view/_cohort_variant_viewer.html">gpsea.view._cohort_variant_viewer</a></li>
 <li><a href="gpsea/view/_disease.html">gpsea.view._disease</a></li>
 <li><a href="gpsea/view/_formatter.html">gpsea.view._formatter</a></li>
+<li><a href="gpsea/view/_phenotype_analysis.html">gpsea.view._phenotype_analysis</a></li>
 <li><a href="gpsea/view/_protein_viewer.html">gpsea.view._protein_viewer</a></li>
 <li><a href="gpsea/view/_protein_visualizable.html">gpsea.view._protein_visualizable</a></li>
 <li><a href="gpsea/view/_protein_visualizer.html">gpsea.view._protein_visualizer</a></li>
diff --git a/stable/_sources/apidocs/gpsea.data.rst.txt b/stable/_sources/apidocs/gpsea.data.rst.txt
deleted file mode 100644
index 2940ee0e8..000000000
--- a/stable/_sources/apidocs/gpsea.data.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-gpsea.data package
-==================
-
-.. automodule:: gpsea.data
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/stable/_sources/apidocs/gpsea.rst.txt b/stable/_sources/apidocs/gpsea.rst.txt
index 69d0030f8..ba30e3729 100644
--- a/stable/_sources/apidocs/gpsea.rst.txt
+++ b/stable/_sources/apidocs/gpsea.rst.txt
@@ -13,7 +13,6 @@ Subpackages
    :maxdepth: 2
 
    gpsea.analysis
-   gpsea.data
    gpsea.model
    gpsea.preprocessing
    gpsea.view
diff --git a/stable/_sources/index.rst.txt b/stable/_sources/index.rst.txt
index f9478fa29..5bcadd386 100644
--- a/stable/_sources/index.rst.txt
+++ b/stable/_sources/index.rst.txt
@@ -10,8 +10,8 @@ A key question in biology and human genetics concerns the relationships between
 genetics, the focus is generally placed on the study of whether specific disease-causing alleles are associated with specific phenotypic 
 manifestations of the disease. 
 
-`GPSEA`  (genotypes and phenotypes - study and evaluation of associations) is a Python package designed to support genotype-phenotype correlation analysis.
-We pronounce GPSEA as "G"-"P"-"C". The input to `GPSEA` is a collection of `Global Alliance for Genomics and Health (GA4GH) Phenopackets <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_.
+`GPSEA`  (Genotypes and Phenotypes - Statistical Evaluation of Associations, pronounced "G"-"P"-"C") is a Python package designed to support genotype-phenotype correlation analysis.
+The input to `GPSEA` is a collection of `Global Alliance for Genomics and Health (GA4GH) Phenopackets <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_.
 `gpsea` ingests data from these phenopackets and performs analysis of the correlation of specific variants,
 variant types (e.g., missense vs. premature termination codon), or variant location in protein motifs or other features.
 The phenotypic abnormalities are represented by `Human Phenotype Ontology (HPO) <https://hpo.jax.org/app/>`_ terms.
diff --git a/stable/_sources/tutorial.rst.txt b/stable/_sources/tutorial.rst.txt
index 0a583b39e..54bf4bc89 100644
--- a/stable/_sources/tutorial.rst.txt
+++ b/stable/_sources/tutorial.rst.txt
@@ -84,7 +84,7 @@ a :class:`~gpsea.model.Cohort`:
 ...     phenopackets=phenopackets,
 ...     cohort_creator=cohort_creator,
 ... )
-Patients Created: ...
+Individuals Processed: ...
 
 and we will check that there are no Q/C issues:
 
@@ -103,7 +103,13 @@ We loaded the patient data into a `cohort` which is ready for the next steps.
 Explore cohort
 ^^^^^^^^^^^^^^
 
-We can now explore the cohort to see how many patients are included.
+GPSEA helps with gaining insight into the cohort by providing 
+
+
+Show cohort summary
+-------------------
+
+The summary report provides an overview about the HPO terms, variants, diseases, and variant effects that occurr most frequently:
 
 >>> from gpsea.view import CohortViewable
 >>> viewer = CohortViewable(hpo)
@@ -121,6 +127,10 @@ We can now explore the cohort to see how many patients are included.
     from IPython.display import HTML, display
     display(HTML(report))
 
+
+Plot distribution of variants with respect to the protein sequence
+------------------------------------------------------------------
+
 Now we can show the distribution of variants with respect to the encoded protein.
 We first obtain `tx_coordinates` (:class:`~gpsea.model.TranscriptCoordinates`)
 and `protein_meta` (:class:`~gpsea.model.ProteinMetadata`)
@@ -154,25 +164,44 @@ and we follow with plotting the diagram of the mutations on the protein:
    :width: 600px
 
 
+.. _show-cohort-variants:
+
+Summarize all variant alleles
+-----------------------------
+
+We can prepare a table of all variant alleles that occurr in the cohort.
+Each table row corresponds to a single allele and lists the variant key,
+the predicted effect on the transcript (*cDNA*) and protein of interest,
+the variant effects, and the number of patients who present
+with one or more variant alleles (*Count*):
+
+>>> from gpsea.view import CohortVariantViewer
+>>> viewer = CohortVariantViewer(tx_id=tx_id)
+>>> report = viewer.process(cohort=cohort)
+>>> with open('docs/report/tbx5_all_variants.html', 'w') as fh:  # doctest: +SKIP
+...     _ = fh.write(report)
+
+.. raw:: html
+  :file: report/tbx5_all_variants.html
+
+
 Prepare genotype and phenotype predicates
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 We will create a predicate to bin patients into group
-depending on presence of a missense and frameshift variant to test
+depending on presence of a single allele of a missense or frameshift variant to test
 if there is a difference between frameshift and non-frameshift variants
 in the individuals of the *TBX5* cohort.
 
 >>> from gpsea.model import VariantEffect
->>> from gpsea.analysis.predicate.genotype import VariantPredicates, groups_predicate
->>> gt_predicate = groups_predicate(
-...     predicates=(
-...         VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id),
-...         VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id)
-...     ),
-...     group_names=('Missense', 'Frameshift'),
+>>> from gpsea.analysis.predicate.genotype import VariantPredicates, monoallelic_predicate
+>>> gt_predicate = monoallelic_predicate(
+...     a_predicate=VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id),
+...     b_predicate=VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id),
+...     names=('Missense', 'Frameshift')
 ... )
 >>> gt_predicate.display_question()
-'Genotype group: Missense, Frameshift'
+'Allele group: Missense, Frameshift'
 
 .. note::
 
@@ -246,15 +275,15 @@ Now we can perform the analysis and investigate the results.
 ...     pheno_predicates=pheno_predicates,
 ... )
 >>> result.total_tests
-17
+16
 
-We only tested 1y HPO terms. This is despite the individuals being collectively annotated with
+We only tested 16 HPO terms. This is despite the individuals being collectively annotated with
 260 direct and indirect HPO terms
 
 >>> len(result.phenotypes)
 260
 
-We can show the reasoning behind *not* testing 243 (`260 - 17`) HPO terms
+We can show the reasoning behind *not* testing 244 (`260 - 16`) HPO terms
 by exploring the phenotype MTC filtering report.
 
 >>> from gpsea.view import MtcStatsViewer
@@ -266,11 +295,11 @@ by exploring the phenotype MTC filtering report.
 .. raw:: html
   :file: report/tbx5_frameshift_vs_missense.mtc_report.html
 
-and these are the top 20 HPO terms ordered by the p value corrected with the Benjamini-Hochberg procedure:
+and these are the tested HPO terms ordered by the p value corrected with the Benjamini-Hochberg procedure:
 
->>> from gpsea.analysis.predicate import PatientCategories
->>> summary_df = result.summarize(hpo, PatientCategories.YES)
->>> summary_df.head(20).to_csv('docs/report/tbx5_frameshift_vs_missense.csv')  # doctest: +SKIP
+>>> from gpsea.view import summarize_hpo_analysis
+>>> summary_df = summarize_hpo_analysis(hpo, result)
+>>> summary_df.to_csv('docs/report/tbx5_frameshift_vs_missense.csv')  # doctest: +SKIP
 
 .. csv-table:: *TBX5* frameshift vs missense
    :file: report/tbx5_frameshift_vs_missense.csv
@@ -283,4 +312,4 @@ was observed in 31/60 (52%) patients with a missense variant
 but it was observed in 19/19 (100%) patients with a frameshift variant.
 Fisher exact test computed a p value of `~0.0000562`
 and the p value corrected by Benjamini-Hochberg procedure
-is `~0.000955`.
+is `~0.000899`.
diff --git a/stable/_sources/user-guide/index.rst.txt b/stable/_sources/user-guide/index.rst.txt
index f3e0569ab..08097f40f 100644
--- a/stable/_sources/user-guide/index.rst.txt
+++ b/stable/_sources/user-guide/index.rst.txt
@@ -4,7 +4,13 @@
 User guide
 ==========
 
-TODO - write high level overview and bridge to individual sections.
+GPSEA allows users to perform many different kinds of genotype-phenotype correlation (GPCs) analysis. See the :ref:`tutorial` for an introduction.
+In general, the analysis will include steps for data input, exploration of the cohort to assist in generating hypotheses about potential GPCs to test, 
+corresponding choice of genotype and phenotype predicates to perform the test, choice of statistical test, and approach to multiple-testing correction (mtc).
+The pages shown in the table of contents provide more information about each step.
+
+
+
 
 .. toctree::
   :maxdepth: 1
@@ -13,7 +19,6 @@ TODO - write high level overview and bridge to individual sections.
   input-data
   exploratory
   predicates
-  phenotype_predicates
   stats
   mtc
   glossary
diff --git a/stable/_sources/user-guide/input-data.rst.txt b/stable/_sources/user-guide/input-data.rst.txt
index b94379b36..1abd1ab8f 100644
--- a/stable/_sources/user-guide/input-data.rst.txt
+++ b/stable/_sources/user-guide/input-data.rst.txt
@@ -80,7 +80,7 @@ loader function:
 
 >>> from gpsea.preprocessing import load_phenopackets
 >>> cohort, qc_results = load_phenopackets(phenopackets, cohort_creator)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-Patients Created: ...
+Individuals Processed: ...
 >>> len(cohort)
 19
 
diff --git a/stable/_sources/user-guide/mtc.rst.txt b/stable/_sources/user-guide/mtc.rst.txt
index 070539d19..7f47e2286 100644
--- a/stable/_sources/user-guide/mtc.rst.txt
+++ b/stable/_sources/user-guide/mtc.rst.txt
@@ -192,62 +192,96 @@ We use static constructor :func:`~gpsea.analysis.mtc_filter.HpoMtcFilter.default
 for creating :class:`~gpsea.analysis.mtc_filter.HpoMtcFilter`.
 The constructor takes a threshold as an argument (e.g. 20% in the example above) 
 and the method's logic is made up of 8 individual heuristics 
-designed to skip testing the HPO terms that are unlikely to yield significant or interesting results:
-
-#. Skip terms that occur very rarely
-    The ``term_frequency_threshold`` determines the mininum proportion of individuals 
-    with direct or indirect annotation by the HPO term to test. 
-    We check each of the genotype groups (e.g., MISSENSE vs. not-MISSENSE), and we only retain a term for testing 
-    if the proportion of individuals in at least one genotype group is greater than or equal to ``term_frequency_threshold``. 
-    
-    This is because of our assumption that even if there is statistical significance, 
-    if a term is only seen in (for example) 7% of individuals in the MISSENSE group and 2% in the not-MISSENSE group, 
-    the term is unlikely to be of great interest because it is rare.
-
-#. Skip terms if no cell has more than one count
-    In a related heuristic, we skip terms if no genotype group has more than one count. 
-    This is not completely redundant with the previous condition, 
-    because some terms may have a small number of total observations.
-
-#. Skip terms if all counts are identical to counts for a child term
-    Let's say a term such as 
-    `Posterior polar cataract (HP:0001115) <https://hpo.jax.org/browse/term/HP:0001115>`_ 
-    was observed in 7 of 11 individuals with MISSENSE variants
-    and in 3 of 8 individuals with NONSENSE variants. 
-    If we find the same patient counts (7 of 11 and 3 of 8) in the parent term 
-    `Polar cataract HP:0010696 <https://hpo.jax.org/browse/term/HP:0010696>`_, 
-    then we choose to not test the parent term. 
-    
-    This is because the more specific an HPO term is, 
-    the more information it has (the more interesting the correlation would be if it exists), 
-    and the result of the Fisher Exact test for *Polar cataract* 
-    would be exactly the same as for *Posterior polar cataract*.
-
-#. Skip terms if genotypes have same HPO proportions
-    If both (or all) of the genotype groups have the same proportion of individuals 
-    observed to be annotated to an HPO term, e.g., both are 50%, then skip the term, 
-    because it is not possible that the Fisher exact test will return a significant result.
-
-#. Skip terms if there are no HPO observations in a group
-    If one of the genotype groups has neither observed nor excluded observations for an HPO term, skip it.
-
-#. Skipping terms that are not descendents of `Phenotypic abnormality (HP:0000118) <https://hpo.jax.org/browse/term/HP:0000118>`_
-    The HPO has a number of other branches that describe modes of inheritance, 
-    past medical history, and clinical modifiers. 
-    We do not think it makes much sense to test for enrichment of these terms, 
-    and so they are filtered out.
-
-#. Skipping "general" level terms 
-    All the direct children of the root phenotype term 
-    `Phenotypic abnormality (HP:0000118) <https://hpo.jax.org/browse/term/HP:0000118>`_ are skipped, 
-    because of the assumption that if there is a valid signal, 
-    it will derive from one of the more specific descendents. 
-    
-    For instance, `Abnormality of the nervous system (HP:0000707) <https://hpo.jax.org/browse/term/HP:0000707>`_
-    is a child of *Phenotypic abnormality*, and this assumption implies 
-    that if there is a signal from the nervous system, 
-    it will lead to at least one of the descendents of 
-    *Abnormality of the nervous system* being significant.
-
-    See :ref:`general-hpo-terms` section for details.
+designed to skip testing the HPO terms that are unlikely to yield significant or interesting results.
 
+
+`HMF01` - Skip terms that occur very rarely
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``term_frequency_threshold`` determines the mininum proportion of individuals
+with direct or indirect annotation by the HPO term to test.
+We check each of the genotype groups (e.g., MISSENSE vs. not-MISSENSE),
+and we only retain a term for testing if the proportion of individuals
+in at least one genotype group is greater than
+or equal to ``term_frequency_threshold``.
+This is because of our assumption that even if there is statistical significance,
+if a term is only seen in (for example) 7% of individuals
+in the MISSENSE group and 2% in the not-MISSENSE group,
+the term is unlikely to be of great interest because it is rare.
+
+
+`HMF02` - Skip terms if no genotype group has more than one count
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In a related heuristic, we skip terms if no genotype group has more 
+than one count. This is not completely redundant with the previous condition,
+because some terms may have a small number of total observations.
+
+
+`HMF03` - Skip terms if all counts are identical to counts for a child term
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Let's say a term such as    
+`Posterior polar cataract (HP:0001115) <https://hpo.jax.org/browse/term/HP:0001115>`_
+was observed in 7 of 11 individuals with MISSENSE variants
+and in 3 of 8 individuals with NONSENSE variants.
+If we find the same patient counts (7 of 11 and 3 of 8) in the parent term
+`Polar cataract HP:0010696 <https://hpo.jax.org/browse/term/HP:0010696>`_,
+then we choose to not test the parent term.
+                                                                                         
+This is because the more specific an HPO term is,
+the more information it has (the more interesting the correlation would be if it exists),
+and the result of a test, such as the Fisher Exact test, would be exactly the same
+for *Polar cataract* as for *Posterior polar cataract*.
+
+
+`HMF04` - Skip terms if genotypes have same HPO proportions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If both (or all) of the genotype groups have the same proportion of individuals
+observed to be annotated to an HPO term, e.g., both are 50%, then skip the term,
+because it is not possible that the Fisher exact test will return a significant result.
+
+
+`HMF05` - Skip term if one of the genotype groups has neither observed nor excluded observations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Skip terms if there are no HPO observations in a group.
+
+
+`HMF06` - Skip term if underpowered for 2x2 or 2x3 analysis
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If the individuals are binned into 2 phenotype groups and 2 genotype groups (2x2)
+and the total count of patients in all genotype-phenotype groups is less than 7,
+or into 2 phenotype groups and 3 genotype groups (2x3) and the total count of patients
+is less than 6, then there is a lack even of the nominal statistical power
+and the counts can never be significant.
+
+
+`HMF07` - Skipping terms that are not descendents of *Phenotypic abnormality*
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The HPO has a number of other branches that describe modes of inheritance,
+past medical history, and clinical modifiers.
+We do not think it makes much sense to test for enrichment of these terms,
+so, all terms that are not descendants of
+`Phenotypic abnormality <https://hpo.jax.org/browse/term/HP:0000118>`_ are filtered out.
+
+
+`HMF08` - Skipping "general" level terms
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+All the direct children of the root phenotype term
+`Phenotypic abnormality (HP:0000118) <https://hpo.jax.org/browse/term/HP:0000118>`_
+are skipped, because of the assumption that if there is a valid signal, 
+it will derive from one of the more specific descendents.
+
+For instance,
+`Abnormality of the nervous system <https://hpo.jax.org/browse/term/HP:0000707>`_
+(HP:0000707) is a child of *Phenotypic abnormality*, and this assumption implies
+that if there is a signal from the nervous system,
+it will lead to at least one of the descendents of
+*Abnormality of the nervous system* being significant.
+
+See :ref:`general-hpo-terms` section for details.
diff --git a/stable/_sources/user-guide/predicates.rst.txt b/stable/_sources/user-guide/predicates.rst.txt
index 785c3ef0c..bfd533b78 100644
--- a/stable/_sources/user-guide/predicates.rst.txt
+++ b/stable/_sources/user-guide/predicates.rst.txt
@@ -4,502 +4,35 @@
 Predicates
 ==========
 
-Searching for genotype-phenotype associations usually requires to partition
-the individuals into several discrete groups to allow testing for the inter-group differences.
+Searching for genotype-phenotype associations usually requires that
+the individuals are partitioned into two or more discrete groups to allow testing for the inter-group differences.
 GPSEA reflects these requirements with its predicate API.
-Perhaps unsurprisingly, a predicate must be capable of partitioning the individuals into two or more groups.
+
+
+A **predicate** must be capable of partitioning the individuals into two or more groups.
 The groups must be *exclusive* - each individual must be assigned at most into one group.
-Moreover, the groups should be *exhaustive* and cover maximum of the possible states.
+In general, it is desirable that the groups cover all or at least the majority of the cohort being analyzed to maximize statistical power.
 However, the predicate is allowed to return `None` if the individual cannot be assigned.
-In result, the individual will be omitted from the downstream analysis.
+As a result, the individual will be omitted from the downstream analysis.
 
-Predicates serve both *genotype* and *phenotype* prongs of the analysis.
+Predicates serve both the *genotype* and *phenotype* prongs of the analysis.
 Genotype predicates (:class:`~gpsea.analysis.predicate.genotype.GenotypePolyPredicate`)
 assign the :class:`~gpsea.model.Patient`
 into a group (mostly) based on the variant information, while the
 phenotype predicates (:class:`~gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate`)
 use the HPO terms to assign a group.
 
-It is literally impossible to use GPSEA without the predicates
-because all analyses need at least one predicate (typically a *genotype* predicate).
-Luckily, the purpose of this guide is to show all that is to know about predicates.
-We will first discuss the genotype predicates and end with phenotype predicates.
-
-.. _genotype-predicates:
-
-*******************
-Genotype predicates
-*******************
-
-A genotype predicate seeks to divide the individuals along an axis that is orthogonal to phenotypes.
-Typically, this includes using the genotype data, such as presence of a missense variant
-in a heterozygous genotype. However, other categorical variables,
-such as diagnoses (TODO - add link to disease predicate) or cluster ids can also be used.
-
-The genotype predicates test the individual for a presence of variants that meet certain inclusion criteria.
-The testing is done in two steps. First, we count the alleles
-of the matching variants and then we interpret the count, possibly including factors
-such as the expected mode of inheritance and sex, to assign the individual into a group.
-Finding the matching variants is what
-the :class:`~gpsea.analysis.predicate.genotype.VariantPredicate` is all about.
-
-
-TODO: wordsmith
-We must first create the variant predicate and then wrap it in genotype predicate.
-
-
-Variant predicates
-==================
-
-GPSEA uses the :class:`~gpsea.analysis.predicate.genotype.VariantPredicate` class
-to test if a :class:`~gpsea.model.Variant` meets the inclusion criteria.
-The variant predicate can leverage multiple primary data:
-
-+------------------------+-------------------------------------------------------------------------------------------------+
-| Primary data source    |   Example                                                                                       |
-+========================+=================================================================================================+
-| Allele                 | the variant being a deletion or a single nucleotide variant (SNV)                               |
-+------------------------+-------------------------------------------------------------------------------------------------+
-| Genome                 | overlaps of a target genomic region                                                             |
-+------------------------+-------------------------------------------------------------------------------------------------+
-| Functional annotation  | variant is predicted to lead to a missense change or affect an exon of certain transcript       |
-+------------------------+-------------------------------------------------------------------------------------------------+
-| Protein data           | variant is located in a region encoding a protein domain, protein feature type                  |
-+------------------------+-------------------------------------------------------------------------------------------------+
-
-which demands a considerable amount of flexibility for creating the predicate.
-
-As a rule of thumb, the predicates for testing basic conditions are available off the shelf,
-and they can be used as building block for testing for more complex conditions,
-such as testing if the variant is "a missense or synonymous variant located in exon 6 of transcript `NM_013275.6`".
-
-Let's demonstrate this on few examples.
-We will load a cohort of 19 subjects with variants in *RERE*,
-leading to `Holt-Oram syndrome MIM:142900 <https://omim.org/entry/142900>`_.
-The the clinical signs and symptoms of the subjects were encoded into HPO terms
-along with the pathogenic *RERE* variant.
-
-Let's load the phenopackets, as previously described in greater detail the :ref:`input-data` section.
-Briefly, we first load HPO:
-
->>> import hpotk
->>> store = hpotk.configure_ontology_store()
->>> hpo = store.load_minimal_hpo(release='v2024-07-01')
-
-then, we configure the cohort creator:
-
->>> from gpsea.preprocessing import configure_caching_cohort_creator
->>> cohort_creator = configure_caching_cohort_creator(hpo)
-
-which we use to create a :class:`~gpsea.model.Cohort` from a bunch of phenopackets
-from the release `0.1.18` of `Phenopacket Store <https://github.com/monarch-initiative/phenopacket-store>`_.
-We will load 19 individuals with mutations in *RERE* gene:
-
->>> from ppktstore.registry import configure_phenopacket_registry
->>> registry = configure_phenopacket_registry()
->>> with registry.open_phenopacket_store(release='0.1.18') as ps:
-...     phenopackets = tuple(ps.iter_cohort_phenopackets('RERE'))
->>> len(phenopackets)
-19
-
-and we will convert the phenopacket into a :class:`~gpsea.model.Cohort`:
-
->>> from gpsea.preprocessing import load_phenopackets
->>> cohort, _ = load_phenopackets(phenopackets, cohort_creator)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-Patients Created: ...
-
-To demonstrate the predicate API, we will use the variant ``1_8358231_8358231_T_C`` that corresponds 
-to a pathogenic variant `VCV000522858.5 <https://www.ncbi.nlm.nih.gov/clinvar/variation/522858/>`_ 
-that replaces the histidine encoded by the 1435th codon of `NM_001042681.2` with arginine: ``NM_001042681.2(RERE):c.4304A>G (p.His1435Arg)``.
-
->>> variant_key_of_interest = '1_8358231_8358231_T_C'
->>> variant = cohort.get_variant_by_key(variant_key_of_interest)
-
-Building blocks
----------------
-
-We can check that the variant overlaps with *RERE*:
-
->>> from gpsea.analysis.predicate.genotype import VariantPredicates
->>> gene = VariantPredicates.gene('RERE')
->>> gene.test(variant)
-True
-
-it overlaps with the *MANE* transcript:
-
->>> rere_mane_tx_id = 'NM_001042681.2'
->>> tx = VariantPredicates.transcript(rere_mane_tx_id)
->>> tx.test(variant)
-True
-
-it in fact overlaps with the exon 20:
-
->>> exon20 = VariantPredicates.exon(exon=20, tx_id=rere_mane_tx_id)
->>> exon20.test(variant)
-True
-
-and leads to a missense mutation with respect to the MANE transcript:
-
->>> from gpsea.model import VariantEffect
->>> missense = VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id=rere_mane_tx_id)
->>> missense.test(variant)
-True
-
-See :class:`~gpsea.analysis.predicate.genotype.VariantPredicates` 
-for more info on the predicates available off the shelf.
-
-
-Complex conditions
-------------------
-
-We can combine the building blocks to test for more elaborate conditions.
-For instance, we can test if the variant meets *any* or several conditions:
-
->>> nonsense = VariantPredicates.variant_effect(VariantEffect.STOP_GAINED, tx_id=rere_mane_tx_id)
->>> missense_or_nonsense = missense | nonsense
->>> missense_or_nonsense.test(variant)
-True
-
-or *all* conditions:
-
->>> missense_and_exon20 = missense & exon20
->>> missense_and_exon20.test(variant)
-True
-
-The `VariantPredicate` overloads Python ``&`` (AND) and ``|`` (OR) operators to build a compound predicate from lower level building blocks.
-
-Therefore, there is nothing that prevents us to combine the predicates into multi-level tests, 
-such as testing if the variant is a *"chromosomal deletion" or a deletion which removes at least 50 bp*:
-
->>> from gpsea.model import VariantClass
->>> chromosomal_deletion = "SO:1000029"
->>> predicate = VariantPredicates.structural_type(chromosomal_deletion) | (VariantPredicates.variant_class(VariantClass.DEL) & VariantPredicates.change_length("<=", -50))
->>> predicate.get_question()
-'(structural type is SO:1000029 OR (variant class is DEL AND change length <= -50))'
-
-
-Inverting conditions
---------------------
-
-Sometimes we may want to test the variant for a condition that must *not* be met.
-For instance, we may want to test if the variant is a deletion 
-that is *not* predicted to shift the transcript reading frame.
-One of doing this would be to build a compound predicates 
-for all variant effects except of :class:`~gpsea.model.VariantEffect.FRAMESHIFT_VARIANT`:
-
->>> non_frameshift_effects = (
-...   VariantEffect.SYNONYMOUS_VARIANT, VariantEffect.MISSENSE_VARIANT, VariantEffect.INTRON_VARIANT,
-...   # and many more effects..
-... )
->>> non_frameshift_predicate = VariantPredicates.all(VariantPredicates.variant_effect(eff, tx_id=rere_mane_tx_id) for eff in non_frameshift_effects)
-
-However, this is clearly tedious and it would be much better implemented 
-by a simple logical not of a predicate for a frameshift variant effect.
-
-To support this, `VariantPredicate` implements *logical inversion* 
-which corresponds to Python's ``~`` operator (tilde), to wrap
-the underlying predicate and to invert its test result.
-
-This is how we can use the predicate inversion to build the predicate for non-frameshift deletions:
-
->>> non_frameshift_del = ~VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id=rere_mane_tx_id) & VariantPredicates.variant_class(VariantClass.DEL)
->>> non_frameshift_del.get_question()
-'(NOT FRAMESHIFT_VARIANT on NM_001042681.2 AND variant class is DEL)'
-
-Note the presence of a tilde ``~`` before the variant effect predicate and resulting ``NOT`` in the predicate question.
-
-The variant predicate offers a flexible API for testing if variants meet a condition.
-However, the genotype phenotype correlations are done on the individual level
-and the variant predicates are used as a component of the genotype predicate.
-The next sections show how to use variant predicates to assign individuals into groups.
-
-
-Mode of inheritance predicate
-=============================
-
-The :class:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate`
-assigns the individual into a group based on the number of alleles
-that match a condition specified by a :class:`~gpsea.analysis.predicate.genotype.VariantPredicate`.
-The :class:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate` supports
-the following Mendelian modes of inheritance (MoI):
-
-
-+-----------------------+-----------------------------------+------------------+------------------------+
-|  Mode of inheritance  | Sex                               |   Allele count   |  Genotype category     |
-+=======================+===================================+==================+========================+
-|  Autosomal dominant   | `*`                               |   0              |  `HOM_REF`             |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   1              |  `HET`                 |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   :math:`\ge 2`  |  ``None``              |
-+-----------------------+-----------------------------------+------------------+------------------------+
-|  Autosomal recessive  | `*`                               |   0              |  `HOM_REF`             |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   1              |  `HET`                 |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   2              |  `BIALLELIC_ALT`       |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   :math:`\ge 3`  |  ``None``              |
-+-----------------------+-----------------------------------+------------------+------------------------+
-|  X-linked dominant    | `*`                               |   0              |  `HOM_REF`             |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   1              |  `HET`                 |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | `*`                               |   :math:`\ge 2`  |  ``None``              |
-+-----------------------+-----------------------------------+------------------+------------------------+
-|  X-linked recessive   | `*`                               |   0              |  `HOM_REF`             |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | :class:`~gpsea.model.Sex.FEMALE`  |   1              |  `HET`                 |
-+                       +                                   +------------------+------------------------+
-|                       |                                   |   2              |  `BIALLELIC_ALT`       |
-+                       +                                   +------------------+------------------------+
-|                       |                                   |   :math:`\ge 3`  |  ``None``              |
-+                       +-----------------------------------+------------------+------------------------+
-|                       | :class:`~gpsea.model.Sex.MALE`    |   1              |  `HEMI`                |
-+                       +                                   +------------------+------------------------+
-|                       |                                   |   :math:`\ge 2`  |  ``None``              |
-+-----------------------+-----------------------------------+------------------+------------------------+
-
-.. note::
-
-    `BIALLELIC_ALT` includes both homozygous and compound heterozygous genotypes.
-
-Clinical judgment should be used to choose the MoI for the cohort analysis.
-Then a predicate for the desired MoI can be created by one of 
-:class:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate` static constructors:
-
-* :func:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant`
-* :func:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive`
-* :func:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant`
-* :func:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive`
-
-All constructors take an instance
-of :class:`~gpsea.analysis.predicate.genotype.VariantPredicate` as an argument.
-
-
-Example
--------
-
-Here we show seting up a predicate for grouping individuals based on
-having a variant that leads to a frameshift or to a stop gain to a fictional transcript ``NM_1234.5``
-to test differences between the genotypes of a disease with an autosomal recessive MoI.
-
-First, we set up a :class:`~gpsea.analysis.predicate.genotype.VariantPredicate`
-for testing if a variant meets the condition:
-
->>> from gpsea.model import VariantEffect
->>> from gpsea.analysis.predicate.genotype import VariantPredicates
->>> tx_id = 'NM_1234.5'
->>> is_frameshift_or_stop_gain = VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id) \
-...     | VariantPredicates.variant_effect(VariantEffect.STOP_GAINED, tx_id)
->>> is_frameshift_or_stop_gain.get_question()
-'(FRAMESHIFT_VARIANT on NM_1234.5 OR STOP_GAINED on NM_1234.5)'
-
-Next, we use :class:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive`
-for assigning a patient into a genotype group:
-
->>> from gpsea.analysis.predicate.genotype import ModeOfInheritancePredicate
->>> gt_predicate = ModeOfInheritancePredicate.autosomal_recessive(is_frameshift_or_stop_gain)
->>> gt_predicate.display_question()
-'Which genotype group does the patient fit in: HOM_REF, HET, BIALLELIC_ALT'
-
-The `gt_predicate` can be used in downstream analysis, such as in :class:
-
-
-.. _filtering-predicate:
-
-Filtering predicate
-===================
-
-Sometimes a predicate can bin individuals into more genotype groups than necessary and there may be need
-to consider only a subset of the groups. A `GenotypePolyPredicate`
-created by :class:`~gpsea.analysis.predicate.genotype.filtering_predicate` can retain only a subset
-of the target categorizations of interest.
-
-Example
--------
-
-Let's suppose we want test the genotype-phenotype association between variants
-that lead to frameshift or a stop gain in a fictional transcript `NM_1234.5`,
-and we are specifically interested in comparing the heterozygous variants
-in a biallelic alternative allele genotypes (homozygous alternate and compound heterozygous).
-
-First, we set up a :class:`~gpsea.analysis.predicate.genotype.VariantPredicate`
-for testing if a variant introduces a premature stop codon or leads to the shift of the reading frame:
-
->>> from gpsea.model import VariantEffect
->>> from gpsea.analysis.predicate.genotype import VariantPredicates
->>> tx_id = 'NM_1234.5'
->>> is_frameshift_or_stop_gain = VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id) \
-...     | VariantPredicates.variant_effect(VariantEffect.STOP_GAINED, tx_id)
->>> is_frameshift_or_stop_gain.get_question()
-'(FRAMESHIFT_VARIANT on NM_1234.5 OR STOP_GAINED on NM_1234.5)'
-
-Then, we create :class:`~gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive`
-to bin according to a genotype group:
-
->>> from gpsea.analysis.predicate.genotype import ModeOfInheritancePredicate
->>> gt_predicate = ModeOfInheritancePredicate.autosomal_recessive(is_frameshift_or_stop_gain)
->>> gt_predicate.display_question()
-'Which genotype group does the patient fit in: HOM_REF, HET, BIALLELIC_ALT'
-
-We see that the `gt_predicate` bins the patients into three groups:
-
->>> cats = gt_predicate.get_categorizations()
->>> cats
-(Categorization(category=HOM_REF), Categorization(category=HET), Categorization(category=BIALLELIC_ALT))
-
-We wrap the categorizations of interest along with the `gt_predicate` by the `filtering_predicate` function,
-and we will get a :class:`~gpsea.analysis.predicate.genotype.GenotypePolyPredicate`
-that includes only the categories of interest:
-
->>> from gpsea.analysis.predicate.genotype import filtering_predicate
->>> fgt_predicate = filtering_predicate(
-...     predicate=gt_predicate,
-...     targets=(cats[1], cats[2]),
-... )
->>> fgt_predicate.display_question()
-'Which genotype group does the patient fit in: HET, BIALLELIC_ALT'
-
-
-.. _groups-predicate:
-
-Groups predicate
-================
-
-Sometimes, all we want is to compare if there is a difference between individuals
-who include one or more alleles of variant $X$ vs. individuals with variants $Y$,
-vs. individuals with variants $Z$, where $X$, $Y$ and $Z$ are variant predicates.
-We can do this with a *groups* predicate.
-
-The :func:`~gpsea.analysis.predicate.genotype.groups_predicate`
-takes *n* variant predicates and *n* group labels, and it will assign the patients
-into the respective groups if one or more matching allele is found.
-However, only one predicate is allowed to return a non-zero allele count.
-Otherwise, the patient is assigned with ``None`` and excluded from the analysis.
-
-Example
--------
-
-Here we show how to build a :class:`~gpsea.analysis.predicate.genotype.GenotypePolyPredicate`
-for testing if the individual has at least one missense vs. frameshift vs. synonymous variant.
-
->>> from gpsea.model import VariantEffect
->>> from gpsea.analysis.predicate.genotype import VariantPredicates, groups_predicate
->>> tx_id = 'NM_1234.5'
->>> gt_predicate = groups_predicate(
-...     predicates=(
-...         VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id),
-...         VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id),
-...         VariantPredicates.variant_effect(VariantEffect.SYNONYMOUS_VARIANT, tx_id),
-...     ),
-...     group_names=('Missense', 'Frameshift', 'Synonymous'),
-... )
->>> gt_predicate.display_question()
-'Genotype group: Missense, Frameshift, Synonymous'
-
-
-.. _sex-predicate:
-
-Partition by the sex of the individual
-======================================
-
-It is easy to investigate the phenotypic differences between females and males.
-The :func:`~gpsea.analysis.predicate.genotype.sex_predicate` provides a predicate
-for partitioning based on the sex of the individual:
-
->>> from gpsea.analysis.predicate.genotype import sex_predicate
->>> gt_predicate = sex_predicate()
->>> gt_predicate.display_question()
-'Sex of the individual: FEMALE, MALE'
-
-The individuals with :class:`~gpsea.model.Sex.UNKNOWN_SEX` will be omitted from the analysis.
-
-
-.. _diagnosis-predicate:
-
-Partition by a diagnosis
-========================
-
-It is also possible to bin the individuals based on a diagnosis.
-The :func:`~gpsea.analysis.predicate.genotype.diagnosis_predicate` 
-prepares a genotype predicate for assigning an individual into a diagnosis group:
-
->>> from gpsea.analysis.predicate.genotype import diagnosis_predicate
->>> gt_predicate = diagnosis_predicate(
-...     diagnoses=('OMIM:154700', 'OMIM:129600'),
-...     labels=('Marfan syndrome', 'Ectopia lentis, familial'),
-... )
->>> gt_predicate.display_question()
-'What disease was diagnosed: OMIM:154700, OMIM:129600'
-
-Note, an individual must match only one diagnosis group. Any individuals labeled with two or more diagnoses
-(e.g. an individual with both *Marfan syndrome* and *Ectopia lentis, familial*)
-will be automatically omitted from the analysis.
-
-
-.. _phenotype-predicates:
-
-********************
-Phenotype predicates
-********************
-
-The phenotype predicate assigns the individual into a group with respect to tested phenotype.
-Typically, the phenotype corresponds to a clinical sign or symptom encoded into an HPO term.
-
-
-Propagating phenotype predicate
-===============================
-
-When testing for presence or absence of an HPO term, the propagating phenotype predicate
-leverages the :ref:`true-path-rule` to take advantage of the HPO hierarchy.
-In result, an individual annotated with a term is implicitly annotated with all its ancestors.
-For instance, an individual annotated with `Ectopia lentis <https://hpo.jax.org/browse/term/HP:0001083>`_
-is also annotated with `Abnormal lens morphology <https://hpo.jax.org/browse/term/HP:0000517>`_,
-`Abnormal anterior eye segment morphology <https://hpo.jax.org/browse/term/HP:0004328>`_,
-`Abnormal eye morphology <https://hpo.jax.org/browse/term/HP:0012372>`_, ...
-
-Similarly, all descendants of a term, whose presence was specifically excluded in an individual,
-are implicitly excluded.
-
-:class:`~gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate` implements this logic.
-
-Example
--------
-
-Here we show how to set up :class:`~gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate`
-to test for a presence of `Abnormal lens morphology <https://hpo.jax.org/browse/term/HP:0000517>`_.
-
-
->>> from gpsea.analysis.predicate.phenotype import PropagatingPhenotypePredicate
->>> query = hpotk.TermId.from_curie('HP:0000517')
->>> pheno_predicate = PropagatingPhenotypePredicate(
-...     hpo=hpo,
-...     query=query,
-... )
->>> pheno_predicate.display_question()
-'Is Abnormal lens morphology present in the patient: Yes, No'
-
-
-TODO: explain ``missing_implies_phenotype_excluded``
-
+All GPSEA analyses need at least one predicate (typically a *genotype* predicate) and many require both *genotype* and *phenotype* predicates.
+The following pages provide more information.
 
-Predicates for all cohort phenotypes
-====================================
 
-Constructing phenotype predicates for all HPO terms of a cohort sounds a bit tedious.
-The :func:`~gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest`
-function cuts down the tedium:
 
->>> from gpsea.analysis.predicate.phenotype import prepare_predicates_for_terms_of_interest
->>> pheno_predicates = prepare_predicates_for_terms_of_interest(
-...     cohort=cohort,
-...     hpo=hpo,
-... )
->>> len(pheno_predicates)
-301
+.. toctree::
+  :maxdepth: 1
+  :caption: Contents:
 
-and prepares predicates for testing 301 HPO terms of the *RERE* cohort.
+  predicates/phenotype_predicates
+  predicates/genotype_predicates
 
 
 *******
diff --git a/stable/_sources/user-guide/devries.rst.txt b/stable/_sources/user-guide/predicates/devries.rst.txt
similarity index 100%
rename from stable/_sources/user-guide/devries.rst.txt
rename to stable/_sources/user-guide/predicates/devries.rst.txt
diff --git a/stable/_sources/user-guide/predicates/diagnosis_predicate.rst.txt b/stable/_sources/user-guide/predicates/diagnosis_predicate.rst.txt
new file mode 100644
index 000000000..386af20a0
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/diagnosis_predicate.rst.txt
@@ -0,0 +1,21 @@
+.. _diagnosis-predicate:
+
+========================
+Partition by a diagnosis
+========================
+
+It is also possible to bin the individuals based on a diagnosis.
+The :func:`~gpsea.analysis.predicate.genotype.diagnosis_predicate` 
+prepares a genotype predicate for assigning an individual into a diagnosis group:
+
+>>> from gpsea.analysis.predicate.genotype import diagnosis_predicate
+>>> gt_predicate = diagnosis_predicate(
+...     diagnoses=('OMIM:154700', 'OMIM:129600'),
+...     labels=('Marfan syndrome', 'Ectopia lentis, familial'),
+... )
+>>> gt_predicate.display_question()
+'What disease was diagnosed: OMIM:154700, OMIM:129600'
+
+Note, an individual must match only one diagnosis group. Any individuals labeled with two or more diagnoses
+(e.g. an individual with both *Marfan syndrome* and *Ectopia lentis, familial*)
+will be automatically omitted from the analysis.
\ No newline at end of file
diff --git a/stable/_sources/user-guide/predicates/genotype_predicates.rst.txt b/stable/_sources/user-guide/predicates/genotype_predicates.rst.txt
new file mode 100644
index 000000000..f1ff3bf74
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/genotype_predicates.rst.txt
@@ -0,0 +1,32 @@
+.. _genotype-predicates:
+
+===================
+Genotype Predicates
+===================
+
+
+A genotype predicate seeks to divide the individuals along an axis that is orthogonal to phenotypes.
+Typically, this includes using the genotype data, such as presence of a missense variant
+in a heterozygous genotype. However, other categorical variables,
+such as diagnoses (TODO - add link to disease predicate) or cluster ids can also be used.
+
+The genotype predicates test the individual for a presence of variants that meet certain inclusion criteria.
+The testing is done in two steps. First, we count the alleles
+of the matching variants and then we interpret the count, possibly including factors
+such as the expected mode of inheritance and sex, to assign the individual into a group.
+Finding the matching variants is what
+the :class:`~gpsea.analysis.predicate.genotype.VariantPredicate` is all about.
+
+
+.. toctree::
+  :maxdepth: 1
+  :caption: Contents:
+
+  variant_predicates
+  mode_of_inheritance_predicate
+  male_female_predicate
+  diagnosis_predicate
+  groups_predicate
+
+
+
diff --git a/stable/_sources/user-guide/predicates/groups_predicate.rst.txt b/stable/_sources/user-guide/predicates/groups_predicate.rst.txt
new file mode 100644
index 000000000..a61428976
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/groups_predicate.rst.txt
@@ -0,0 +1,41 @@
+.. _groups-predicate:
+
+================
+Groups Predicate
+================
+
+
+
+Sometimes, all we want is to compare if there is a difference between individuals
+who include one or more alleles of variant `X` vs. individuals with variants `Y`,
+vs. individuals with variants `Z`, where `X`, `Y` and `Z` are variant predicates.
+We can do this with a *groups* predicate.
+
+The :func:`~gpsea.analysis.predicate.genotype.groups_predicate`
+takes *n* variant predicates and *n* group labels, and it will assign the patients
+into the respective groups if one or more matching allele is found.
+However, only one predicate is allowed to return a non-zero allele count.
+Otherwise, the patient is assigned with ``None`` and excluded from the analysis.
+
+Example
+-------
+
+Here we show how to build a :class:`~gpsea.analysis.predicate.genotype.GenotypePolyPredicate`
+for testing if the individual has at least one missense vs. frameshift vs. synonymous variant.
+
+>>> from gpsea.model import VariantEffect
+>>> from gpsea.analysis.predicate.genotype import VariantPredicates, groups_predicate
+>>> tx_id = 'NM_1234.5'
+>>> gt_predicate = groups_predicate(
+...     predicates=(
+...         VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id),
+...         VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id),
+...         VariantPredicates.variant_effect(VariantEffect.SYNONYMOUS_VARIANT, tx_id),
+...     ),
+...     group_names=('Missense', 'Frameshift', 'Synonymous'),
+... )
+>>> gt_predicate.display_question()
+'Genotype group: Missense, Frameshift, Synonymous'
+
+
+
diff --git a/stable/_sources/user-guide/predicates/hpo_predicate.rst.txt b/stable/_sources/user-guide/predicates/hpo_predicate.rst.txt
new file mode 100644
index 000000000..a5fc0549a
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/hpo_predicate.rst.txt
@@ -0,0 +1,87 @@
+.. _hpo-predicate:
+
+
+HPO predicate
+=============
+
+When testing for presence or absence of an HPO term, the :class:`~gpsea.analysis.predicate.phenotype.HpoPredicate`
+leverages the :ref:`true-path-rule` to take advantage of the HPO hierarchy.
+In result, an individual annotated with a term is implicitly annotated with all its ancestors.
+For instance, an individual annotated with `Ectopia lentis <https://hpo.jax.org/browse/term/HP:0001083>`_
+is also annotated with `Abnormal lens morphology <https://hpo.jax.org/browse/term/HP:0000517>`_,
+`Abnormal anterior eye segment morphology <https://hpo.jax.org/browse/term/HP:0004328>`_,
+`Abnormal eye morphology <https://hpo.jax.org/browse/term/HP:0012372>`_, ...
+
+Similarly, all descendants of a term, whose presence was specifically excluded in an individual,
+are implicitly excluded.
+
+Example
+-------
+
+Here we show how to set up :class:`~gpsea.analysis.predicate.phenotype.HpoPredicate`
+to test for a presence of `Abnormal lens morphology <https://hpo.jax.org/browse/term/HP:0000517>`_.
+
+We need to load :class:`~hpotk.MinimalOntology` with HPO data to access the HPO hierarchy:
+
+>>> import hpotk
+>>> store = hpotk.configure_ontology_store()
+>>> hpo = store.load_minimal_hpo(release='v2024-07-01')
+
+and now we can set up a predicate to test for presence of *Abnormal lens morphology*:
+
+>>> from gpsea.analysis.predicate.phenotype import HpoPredicate
+>>> query = hpotk.TermId.from_curie('HP:0000517')
+>>> pheno_predicate = HpoPredicate(
+...     hpo=hpo,
+...     query=query,
+... )
+>>> pheno_predicate.display_question()
+'Is Abnormal lens morphology present in the patient: Yes, No'
+
+
+
+missing_implies_phenotype_excluded
+----------------------------------
+
+In many cases, published reports of clinical data about individuals with rare diseases describes phenotypic features that were observed, but do not 
+provide a comprehensive list of features that were explicitly excluded. By default, GPSEA will only include features that are recorded as observed or excluded in a phenopacket.
+Setting this argument to True will cause "n/a" entries to be set to "excluded". We provide this option for exploration but do not recommend its use for the 
+final analysis unless the assumption behind it is known to be true.
+
+
+
+Predicates for all cohort phenotypes
+====================================
+
+Constructing phenotype predicates for all HPO terms of a cohort sounds a bit tedious.
+The :func:`~gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest`
+function cuts down the tedium.
+
+For a given phenopacket collection (e.g. 156 patients with mutations in *WWOX* gene included in Phenopacket Store version `0.1.18`)
+
+>>> from ppktstore.registry import configure_phenopacket_registry
+>>> registry = configure_phenopacket_registry()
+>>> with registry.open_phenopacket_store(release='0.1.18') as ps:
+...     phenopackets = tuple(ps.iter_cohort_phenopackets('TBX5'))
+>>> len(phenopackets)
+156
+
+processed into a cohort
+
+>>> from gpsea.preprocessing import configure_caching_cohort_creator, load_phenopackets
+>>> cohort_creator = configure_caching_cohort_creator(hpo)
+>>> cohort, _ = load_phenopackets(phenopackets, cohort_creator)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
+Individuals Processed: ...
+
+
+we can create HPO predicates for testing all 260 HPO terms used in the cohort
+
+>>> from gpsea.analysis.predicate.phenotype import prepare_predicates_for_terms_of_interest
+>>> pheno_predicates = prepare_predicates_for_terms_of_interest(
+...     cohort=cohort,
+...     hpo=hpo,
+... )
+>>> len(pheno_predicates)
+260
+
+and subject the predicates into further analysis, such as :class:`~gpsea.analysis.pcats.HpoTermAnalysis`.
diff --git a/stable/_sources/user-guide/predicates/male_female_predicate.rst.txt b/stable/_sources/user-guide/predicates/male_female_predicate.rst.txt
new file mode 100644
index 000000000..3bed237ec
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/male_female_predicate.rst.txt
@@ -0,0 +1,21 @@
+.. _male-female-predicate:
+
+Partition by the sex of the individual
+======================================
+
+It is easy to investigate the phenotypic differences between females and males.
+The :func:`~gpsea.analysis.predicate.genotype.sex_predicate` provides a predicate
+for partitioning based on the sex of the individual:
+
+>>> from gpsea.analysis.predicate.genotype import sex_predicate
+>>> gt_predicate = sex_predicate()
+>>> gt_predicate.display_question()
+'Sex of the individual: FEMALE, MALE'
+
+The individuals with :class:`~gpsea.model.Sex.UNKNOWN_SEX` will be omitted from the analysis.
+
+Note that we have implemented this predicate as a genotype predicate, because it is used in 
+place of other genotype predicates. Currently, it is not possible to compare the distribution of genotypes across sexes.
+
+
+
diff --git a/stable/_sources/user-guide/predicates/mode_of_inheritance_predicate.rst.txt b/stable/_sources/user-guide/predicates/mode_of_inheritance_predicate.rst.txt
new file mode 100644
index 000000000..6c4178e8a
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/mode_of_inheritance_predicate.rst.txt
@@ -0,0 +1,93 @@
+.. _mode-of-inheritance-predicate:
+
+==============================
+Mode of Inheritance Predicates
+==============================
+
+There are five basic modes of inheritance for single-gene diseases: autosomal dominant, 
+autosomal recessive, X-linked dominant, X-linked recessive, and mitochondrial 
+(See `Understanding Genetics, Appendix B <https://www.ncbi.nlm.nih.gov/books/NBK132145/>`_).
+
+
+The :class:`~gpsea.analysis.predicate.genotype.autosomal_dominant`
+and :class:`~gpsea.analysis.predicate.genotype.autosomal_recessive`
+assigns the individual into a group based on the number of the alleles
+observed in the individual.
+GPSEA supports the following Mendelian modes of inheritance (MoI):
+
+
++-----------------------+------------------+------------------------+
+|  Mode of inheritance  |   Allele count   |  Genotype category     |
++=======================+==================+========================+
+|  Autosomal dominant   |   0              |  `HOM_REF`             |
++                       +------------------+------------------------+
+|                       |   1              |  `HET`                 |
++                       +------------------+------------------------+
+|                       |   :math:`\ge 2`  |  ``None``              |
++-----------------------+------------------+------------------------+
+|  Autosomal recessive  |   0              |  `HOM_REF`             |
++                       +------------------+------------------------+
+|                       |   1              |  `HET`                 |
++                       +------------------+------------------------+
+|                       |   2              |  `BIALLELIC_ALT`       |
++                       +------------------+------------------------+
+|                       |   :math:`\ge 3`  |  ``None``              |
++-----------------------+------------------+------------------------+
+
+
+.. note::
+
+    `BIALLELIC_ALT` includes both homozygous and compound heterozygous genotypes.
+
+Clinical judgment should be used to choose the MoI for the cohort analysis.
+Then a predicate for the desired MoI can be created by calling one
+of the following methods:
+
+* :func:`~gpsea.analysis.predicate.genotype.autosomal_dominant`
+* :func:`~gpsea.analysis.predicate.genotype.autosomal_recessive`
+
+By default, the MoI predicates will use *all* variants recorded in the individual.
+However, a :class:`~gpsea.analysis.predicate.genotype.VariantPredicate`
+can be provided to select a variant subset, if necessary.
+
+
+Assign individuals into genotype groups
+---------------------------------------
+
+Here we show seting up a predicate for grouping individuals for differences
+between genotypes of a disease with an autosomal recessive MoI.
+
+We use :class:`~gpsea.analysis.predicate.genotype.autosomal_recessive`
+to create the predicate:
+
+>>> from gpsea.analysis.predicate.genotype import autosomal_recessive
+>>> gt_predicate = autosomal_recessive()
+>>> gt_predicate.display_question()
+'What is the genotype group: HOM_REF, HET, BIALLELIC_ALT'
+
+The predicate will use *all* recorded variants to determine if the individual belongs into
+homozygous reference (`HOM_REF`), heterozygous (`HET`), or biallelic alternative (`BIALLELIC_ALT`)
+category.
+
+
+Use a subset of variants for choosing the genotype group
+--------------------------------------------------------
+
+To select specific variants, a :class:`~gpsea.analysis.predicate.genotype.VariantPredicate`
+can be registered with the MoI predicate.
+For instance, the following can be done to only consider the variants that lead
+to a missense change on a fictional transcript ``NM_1234.5``
+when assigning the genotype group. We set up the variant predicate:
+
+>>> from gpsea.model import VariantEffect
+>>> from gpsea.analysis.predicate.genotype import VariantPredicates
+>>> tx_id = 'NM_1234.5'
+>>> is_missense = VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id)
+>>> is_missense.get_question()
+'MISSENSE_VARIANT on NM_1234.5'
+
+and we use it to create the MoI predicate:
+
+>>> gt_predicate = autosomal_recessive(is_missense)
+>>> gt_predicate.display_question()
+'What is the genotype group: HOM_REF, HET, BIALLELIC_ALT'
diff --git a/stable/_sources/user-guide/phenotype_predicates.rst.txt b/stable/_sources/user-guide/predicates/phenotype_predicates.rst.txt
similarity index 94%
rename from stable/_sources/user-guide/phenotype_predicates.rst.txt
rename to stable/_sources/user-guide/predicates/phenotype_predicates.rst.txt
index 86572657f..b8991a290 100644
--- a/stable/_sources/user-guide/phenotype_predicates.rst.txt
+++ b/stable/_sources/user-guide/predicates/phenotype_predicates.rst.txt
@@ -15,4 +15,5 @@ TODO -- separate explanations for HPO (Fisher), scores (Mann Whitney) and surviv
   :maxdepth: 1
   :caption: Contents:
 
+  hpo_predicate
   devries
diff --git a/stable/_sources/user-guide/predicates/variant_predicates.rst.txt b/stable/_sources/user-guide/predicates/variant_predicates.rst.txt
new file mode 100644
index 000000000..1053fbbbf
--- /dev/null
+++ b/stable/_sources/user-guide/predicates/variant_predicates.rst.txt
@@ -0,0 +1,168 @@
+.. _variant_predicates:
+
+==================
+Variant Predicates
+==================
+
+
+GPSEA uses the :class:`~gpsea.analysis.predicate.genotype.VariantPredicate` class
+to test if a :class:`~gpsea.model.Variant` meets the inclusion criteria.
+The variant predicate can leverage multiple primary data:
+
++------------------------+-------------------------------------------------------------------------------------------------+
+| Primary data source    |   Example                                                                                       |
++========================+=================================================================================================+
+| Allele                 | the variant being a deletion or a single nucleotide variant (SNV)                               |
++------------------------+-------------------------------------------------------------------------------------------------+
+| Genome                 | overlaps of a target genomic region                                                             |
++------------------------+-------------------------------------------------------------------------------------------------+
+| Functional annotation  | variant is predicted to lead to a missense change or affect an exon of certain transcript       |
++------------------------+-------------------------------------------------------------------------------------------------+
+| Protein data           | variant is located in a region encoding a protein domain, protein feature type                  |
++------------------------+-------------------------------------------------------------------------------------------------+
+
+which demands a considerable amount of flexibility for creating the predicate.
+
+As a rule of thumb, the predicates for testing basic conditions are available off the shelf,
+and they can be used as building block for testing for more complex conditions,
+such as testing if the variant is "a missense or synonymous variant located in exon 6 of transcript `NM_013275.6`".
+
+Let's demonstrate this on few examples.
+We will load a cohort of 19 subjects with variants in *RERE*,
+leading to `Holt-Oram syndrome MIM:142900 <https://omim.org/entry/142900>`_.
+The the clinical signs and symptoms of the subjects were encoded into HPO terms
+along with the pathogenic *RERE* variant.
+
+Let's load the phenopackets, as previously described in greater detail the :ref:`input-data` section.
+Briefly, we first load HPO:
+
+>>> import hpotk
+>>> store = hpotk.configure_ontology_store()
+>>> hpo = store.load_minimal_hpo(release='v2024-07-01')
+
+then, we configure the cohort creator:
+
+>>> from gpsea.preprocessing import configure_caching_cohort_creator
+>>> cohort_creator = configure_caching_cohort_creator(hpo)
+
+which we use to create a :class:`~gpsea.model.Cohort` from a bunch of phenopackets
+from the release `0.1.18` of `Phenopacket Store <https://github.com/monarch-initiative/phenopacket-store>`_.
+We will load 19 individuals with mutations in *RERE* gene:
+
+>>> from ppktstore.registry import configure_phenopacket_registry
+>>> registry = configure_phenopacket_registry()
+>>> with registry.open_phenopacket_store(release='0.1.18') as ps:
+...     phenopackets = tuple(ps.iter_cohort_phenopackets('RERE'))
+>>> len(phenopackets)
+19
+
+and we will convert the phenopacket into a :class:`~gpsea.model.Cohort`:
+
+>>> from gpsea.preprocessing import load_phenopackets
+>>> cohort, _ = load_phenopackets(phenopackets, cohort_creator)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
+Individuals Processed: ...
+
+To demonstrate the predicate API, we will use the variant ``1_8358231_8358231_T_C`` that corresponds 
+to a pathogenic variant `VCV000522858.5 <https://www.ncbi.nlm.nih.gov/clinvar/variation/522858/>`_ 
+that replaces the histidine encoded by the 1435th codon of `NM_001042681.2` with arginine: ``NM_001042681.2(RERE):c.4304A>G (p.His1435Arg)``.
+
+>>> variant_key_of_interest = '1_8358231_8358231_T_C'
+>>> variant = cohort.get_variant_by_key(variant_key_of_interest)
+
+Building blocks
+---------------
+
+We can check that the variant overlaps with *RERE*:
+
+>>> from gpsea.analysis.predicate.genotype import VariantPredicates
+>>> gene = VariantPredicates.gene('RERE')
+>>> gene.test(variant)
+True
+
+it overlaps with the *MANE* transcript:
+
+>>> rere_mane_tx_id = 'NM_001042681.2'
+>>> tx = VariantPredicates.transcript(rere_mane_tx_id)
+>>> tx.test(variant)
+True
+
+it in fact overlaps with the exon 20:
+
+>>> exon20 = VariantPredicates.exon(exon=20, tx_id=rere_mane_tx_id)
+>>> exon20.test(variant)
+True
+
+and leads to a missense mutation with respect to the MANE transcript:
+
+>>> from gpsea.model import VariantEffect
+>>> missense = VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id=rere_mane_tx_id)
+>>> missense.test(variant)
+True
+
+See :class:`~gpsea.analysis.predicate.genotype.VariantPredicates` 
+for more info on the predicates available off the shelf.
+
+
+Complex conditions
+------------------
+
+We can combine the building blocks to test for more elaborate conditions.
+For instance, we can test if the variant meets *any* or several conditions:
+
+>>> nonsense = VariantPredicates.variant_effect(VariantEffect.STOP_GAINED, tx_id=rere_mane_tx_id)
+>>> missense_or_nonsense = missense | nonsense
+>>> missense_or_nonsense.test(variant)
+True
+
+or *all* conditions:
+
+>>> missense_and_exon20 = missense & exon20
+>>> missense_and_exon20.test(variant)
+True
+
+The `VariantPredicate` overloads Python ``&`` (AND) and ``|`` (OR) operators to build a compound predicate from lower level building blocks.
+
+Therefore, there is nothing that prevents us to combine the predicates into multi-level tests, 
+such as testing if the variant is a *"chromosomal deletion" or a deletion which removes at least 50 bp*:
+
+>>> from gpsea.model import VariantClass
+>>> chromosomal_deletion = "SO:1000029"
+>>> predicate = VariantPredicates.structural_type(chromosomal_deletion) | (VariantPredicates.variant_class(VariantClass.DEL) & VariantPredicates.change_length("<=", -50))
+>>> predicate.get_question()
+'(structural type is SO:1000029 OR (variant class is DEL AND change length <= -50))'
+
+
+Inverting conditions
+--------------------
+
+Sometimes we may want to test the variant for a condition that must *not* be met.
+For instance, we may want to test if the variant is a deletion 
+that is *not* predicted to shift the transcript reading frame.
+One of doing this would be to build a compound predicates 
+for all variant effects except of :class:`~gpsea.model.VariantEffect.FRAMESHIFT_VARIANT`:
+
+>>> non_frameshift_effects = (
+...   VariantEffect.SYNONYMOUS_VARIANT, VariantEffect.MISSENSE_VARIANT, VariantEffect.INTRON_VARIANT,
+...   # and many more effects..
+... )
+>>> non_frameshift_predicate = VariantPredicates.all(VariantPredicates.variant_effect(eff, tx_id=rere_mane_tx_id) for eff in non_frameshift_effects)
+
+However, this is clearly tedious and it would be much better implemented 
+by a simple logical not of a predicate for a frameshift variant effect.
+
+To support this, `VariantPredicate` implements *logical inversion* 
+which corresponds to Python's ``~`` operator (tilde), to wrap
+the underlying predicate and to invert its test result.
+
+This is how we can use the predicate inversion to build the predicate for non-frameshift deletions:
+
+>>> non_frameshift_del = ~VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id=rere_mane_tx_id) & VariantPredicates.variant_class(VariantClass.DEL)
+>>> non_frameshift_del.get_question()
+'(NOT FRAMESHIFT_VARIANT on NM_001042681.2 AND variant class is DEL)'
+
+Note the presence of a tilde ``~`` before the variant effect predicate and resulting ``NOT`` in the predicate question.
+
+The variant predicate offers a flexible API for testing if variants meet a condition.
+However, the genotype phenotype correlations are done on the individual level
+and the variant predicates are used as a component of the genotype predicate.
+The next sections show how to use variant predicates to assign individuals into groups.
diff --git a/stable/_sources/user-guide/stats.rst.txt b/stable/_sources/user-guide/stats.rst.txt
index 55757ef30..18882892a 100644
--- a/stable/_sources/user-guide/stats.rst.txt
+++ b/stable/_sources/user-guide/stats.rst.txt
@@ -102,7 +102,7 @@ with the default cohort creator:
 >>> from gpsea.preprocessing import configure_caching_cohort_creator, load_phenopackets
 >>> cohort_creator = configure_caching_cohort_creator(hpo)
 >>> cohort, qc_results = load_phenopackets(phenopackets, cohort_creator)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-Patients Created: ...
+Individuals Processed: ...
 >>> qc_results.summarize()  # doctest: +SKIP
 Validated under none policy
 No errors or warnings were found
@@ -127,7 +127,7 @@ First, we create a :class:`~gpsea.analysis.predicate.genotype.VariantPredicate`
 to test if the variant leads to a frameshift (in this case):
 
 >>> from gpsea.model import VariantEffect
->>> from gpsea.analysis.predicate.genotype import VariantPredicates, boolean_predicate
+>>> from gpsea.analysis.predicate.genotype import VariantPredicates
 >>> tx_id = 'NM_181486.4'
 >>> is_frameshift = VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id)
 >>> is_frameshift.get_question()
@@ -136,10 +136,10 @@ to test if the variant leads to a frameshift (in this case):
 and then we choose the expected mode of inheritance to test. In case of *TBX5*,
 we expect the autosomal dominant mode of inheritance:
 
->>> from gpsea.analysis.predicate.genotype import ModeOfInheritancePredicate
->>> gt_predicate = ModeOfInheritancePredicate.autosomal_dominant(is_frameshift)
+>>> from gpsea.analysis.predicate.genotype import autosomal_dominant
+>>> gt_predicate = autosomal_dominant(is_frameshift)
 >>> gt_predicate.display_question()
-'Which genotype group does the patient fit in: HOM_REF, HET'
+'What is the genotype group: HOM_REF, HET'
 
 `gt_predicate` will assign the patients with no frameshift variant allele into `HOM_REF` group
 and the patients with one frameshift allele will be assigned into `HET` group.
@@ -230,10 +230,10 @@ We can now execute the analysis:
 >>> len(result.phenotypes)
 260
 >>> result.total_tests
-17
+16
 
 
-Thanks to Phenotype MTC filter, we only tested 17 out of 260 terms.
+Thanks to Phenotype MTC filter, we only tested 16 out of 260 terms.
 We can learn more by showing the MTC filter report:
 
 >>> from gpsea.view import MtcStatsViewer
@@ -251,12 +251,11 @@ Genotype phenotype associations
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Last, let's explore the associations. The results include a table with all tested HPO terms
-ordered by the corrected p value (Benjamini-Hochberg FDR).
-Here we show the top 20 table rows:
+ordered by the corrected p value (Benjamini-Hochberg FDR):
 
->>> from gpsea.analysis.predicate import PatientCategories
->>> summary_df = result.summarize(hpo, PatientCategories.YES)
->>> summary_df.head(20).to_csv('docs/user-guide/report/tbx5_frameshift.csv')  # doctest: +SKIP
+>>> from gpsea.view import summarize_hpo_analysis
+>>> summary_df = summarize_hpo_analysis(hpo, result)
+>>> summary_df.to_csv('docs/user-guide/report/tbx5_frameshift.csv')  # doctest: +SKIP
 
 .. csv-table:: *TBX5* frameshift vs rest
    :file: report/tbx5_frameshift.csv
@@ -270,7 +269,7 @@ was observed in 31/60 (52%) patients with a missense variant
 but it was observed in 19/19 (100%) patients with a frameshift variant.
 Fisher exact test computed a p value of `~0.000242`
 and the p value corrected by Benjamini-Hochberg procedure
-is `~0.00411`.
+is `~0.00387`.
 
 The table includes all HPO terms of the cohort, including the terms that were not selected for testing
 and thus have no associated p value.
@@ -345,7 +344,7 @@ which we will use to preprocess the cohort
 
 >>> from gpsea.preprocessing import load_phenopackets
 >>> cohort, _ = load_phenopackets(phenopackets, cohort_creator)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-Patients Created: ...
+Individuals Processed: ...
 
 
 resulting in a cohort consisting of 19 individuals
diff --git a/stable/_static/documentation_options.js b/stable/_static/documentation_options.js
index 7254ddd9f..025330ce9 100644
--- a/stable/_static/documentation_options.js
+++ b/stable/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.3.0',
+    VERSION: '0.4.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/stable/apidocs/gpsea.analysis.html b/stable/apidocs/gpsea.analysis.html
index 4a3cf882c..f7df1a5e7 100644
--- a/stable/apidocs/gpsea.analysis.html
+++ b/stable/apidocs/gpsea.analysis.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="current reference internal" href="#">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -110,6 +109,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l1"><a class="reference internal" href="gpsea.analysis.mtc_filter.html">gpsea.analysis.mtc_filter package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcFilter"><code class="docutils literal notranslate"><span class="pre">PhenotypeMtcFilter</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult"><code class="docutils literal notranslate"><span class="pre">PhenotypeMtcResult</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcIssue"><code class="docutils literal notranslate"><span class="pre">PhenotypeMtcIssue</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter"><code class="docutils literal notranslate"><span class="pre">UseAllTermsMtcFilter</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter"><code class="docutils literal notranslate"><span class="pre">SpecifiedTermsMtcFilter</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter"><code class="docutils literal notranslate"><span class="pre">HpoMtcFilter</span></code></a></li>
diff --git a/stable/apidocs/gpsea.analysis.mtc_filter.html b/stable/apidocs/gpsea.analysis.mtc_filter.html
index f3ae44f51..075f4dc97 100644
--- a/stable/apidocs/gpsea.analysis.mtc_filter.html
+++ b/stable/apidocs/gpsea.analysis.mtc_filter.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.mtc_filter package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.mtc_filter package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -117,6 +116,14 @@
 Therefore, the expected input asks for <code class="xref py py-class docutils literal notranslate"><span class="pre">hpotk.TermId</span></code> items.
 For instance, <cite>n_usable</cite> is a mapping from an <em>HPO term</em> to an <cite>int</cite> with the count of the patients
 categorized according to the HPO term.</p>
+<p><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK" title="gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK"><code class="xref py py-attr docutils literal notranslate"><span class="pre">PhenotypeMtcFilter.OK</span></code></a> is returned for HPO terms that pass MTC filtering
+and <em>should</em> be included in the analysis.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK">
+<span class="sig-name descname"><span class="pre">OK</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=True,</span> <span class="pre">issue=None)</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK" title="Link to this definition"></a></dt>
+<dd><p>The MTC result for the phenotypes that pass the filtering and <em>should</em> be included in the analysis.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter">
 <em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gt_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ph_predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypePolyPredicate"><span class="pre">PhenotypePolyPredicate</span></a><span class="p"><span class="pre">[</span></span><span class="pre">P</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">counts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://pandas.pydata.org/pandas-docs/version/2.0.0/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.0.0)"><span class="pre">DataFrame</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcFilter.filter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter" title="Link to this definition"></a></dt>
@@ -136,6 +143,12 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcFilter.possible_results">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">possible_results</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Collection" title="(in Python v3.12)"><span class="pre">Collection</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcFilter.possible_results"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.possible_results" title="Link to this definition"></a></dt>
+<dd><p>Return all possible result types which the <cite>PhenotypeMtcFilter</cite> can produce.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter_method_name">
 <em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filter_method_name</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcFilter.filter_method_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter_method_name" title="Link to this definition"></a></dt>
@@ -146,11 +159,12 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcResult">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.mtc_filter.</span></span><span class="sig-name descname"><span class="pre">PhenotypeMtcResult</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">status</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">reason</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcResult"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.mtc_filter.</span></span><span class="sig-name descname"><span class="pre">PhenotypeMtcResult</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">status</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">issue</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcIssue" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcIssue"><span class="pre">PhenotypeMtcIssue</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcResult"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p><cite>PhenotypeMtcResult</cite> represents a result of <a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter" title="gpsea.analysis.mtc_filter.PhenotypeMtcFilter"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhenotypeMtcFilter</span></code></a> for a single phenotype.</p>
 <p>The phenotype can either pass the filter, in order to be included in the downstream analysis (<a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_passed" title="gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_passed"><code class="xref py py-meth docutils literal notranslate"><span class="pre">is_passed()</span></code></a>)
-of be filtered out (<a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out" title="gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out"><code class="xref py py-meth docutils literal notranslate"><span class="pre">is_filtered_out()</span></code></a>) in which case <a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason" title="gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason"><code class="xref py py-attr docutils literal notranslate"><span class="pre">reason</span></code></a> must be available.</p>
+of be filtered out (<a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out" title="gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out"><code class="xref py py-meth docutils literal notranslate"><span class="pre">is_filtered_out()</span></code></a>) in which case <a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue" title="gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue"><code class="xref py py-attr docutils literal notranslate"><span class="pre">mtc_issue</span></code></a> with more context
+regarding the culprit must be available.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcResult.ok">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ok</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcResult.ok"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.ok" title="Link to this definition"></a></dt>
@@ -158,7 +172,7 @@
 
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcResult.fail">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">fail</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reason</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcResult.fail"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.fail" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">fail</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">code</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">reason</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcResult.fail"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.fail" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
@@ -171,6 +185,11 @@
 <span class="sig-name descname"><span class="pre">is_filtered_out</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcResult.is_filtered_out"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
+<dl class="py property">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mtc_issue</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcIssue" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcIssue"><span class="pre">PhenotypeMtcIssue</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py property">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">reason</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason" title="Link to this definition"></a></dt>
@@ -178,6 +197,25 @@
 
 </dd></dl>
 
+<dl class="py class">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcIssue">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.mtc_filter.</span></span><span class="sig-name descname"><span class="pre">PhenotypeMtcIssue</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">code</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">reason</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#PhenotypeMtcIssue"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcIssue" title="Link to this definition"></a></dt>
+<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>The container for data available regarding the reason why a phenotype was filtered out.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcIssue.code">
+<span class="sig-name descname"><span class="pre">code</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcIssue.code" title="Link to this definition"></a></dt>
+<dd><p>A <cite>str</cite> with a unique code of the issue.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.PhenotypeMtcIssue.reason">
+<span class="sig-name descname"><span class="pre">reason</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.PhenotypeMtcIssue.reason" title="Link to this definition"></a></dt>
+<dd><p>A human-friendly explanation of the issue.</p>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.UseAllTermsMtcFilter">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.mtc_filter.</span></span><span class="sig-name descname"><span class="pre">UseAllTermsMtcFilter</span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#UseAllTermsMtcFilter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter" title="Link to this definition"></a></dt>
@@ -203,6 +241,12 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.possible_results">
+<span class="sig-name descname"><span class="pre">possible_results</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Collection" title="(in Python v3.12)"><span class="pre">Collection</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#UseAllTermsMtcFilter.possible_results"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.possible_results" title="Link to this definition"></a></dt>
+<dd><p>Return all possible result types which the <cite>PhenotypeMtcFilter</cite> can produce.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter_method_name">
 <span class="sig-name descname"><span class="pre">filter_method_name</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#UseAllTermsMtcFilter.filter_method_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter_method_name" title="Link to this definition"></a></dt>
@@ -221,6 +265,12 @@
 terms to the constructor of this class, thereby preventing other terms from
 being tested and reducing the multiple testing burden.</p>
 <p>See <a class="reference internal" href="../user-guide/mtc.html#specify-terms-strategy"><span class="std std-ref">Specify terms strategy</span></a> section for more info.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.NON_SPECIFIED_TERM">
+<span class="sig-name descname"><span class="pre">NON_SPECIFIED_TERM</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='ST1',</span> <span class="pre">reason='Non-specified</span> <span class="pre">term'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.NON_SPECIFIED_TERM" title="Link to this definition"></a></dt>
+<dd><p>The MTC filtering result returned when an HPO term does not belong among the selection of terms to be tested.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter">
 <span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gt_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ph_predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypePolyPredicate"><span class="pre">PhenotypePolyPredicate</span></a><span class="p"><span class="pre">[</span></span><span class="pre">P</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">counts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://pandas.pydata.org/pandas-docs/version/2.0.0/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.0.0)"><span class="pre">DataFrame</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#SpecifiedTermsMtcFilter.filter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter" title="Link to this definition"></a></dt>
@@ -240,6 +290,12 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.possible_results">
+<span class="sig-name descname"><span class="pre">possible_results</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Collection" title="(in Python v3.12)"><span class="pre">Collection</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#SpecifiedTermsMtcFilter.possible_results"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.possible_results" title="Link to this definition"></a></dt>
+<dd><p>Return all possible result types which the <cite>PhenotypeMtcFilter</cite> can produce.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter_method_name">
 <span class="sig-name descname"><span class="pre">filter_method_name</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#SpecifiedTermsMtcFilter.filter_method_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter_method_name" title="Link to this definition"></a></dt>
@@ -256,6 +312,36 @@
 <p>The class leverages a number of heuristics and domain decisions.
 See <a class="reference internal" href="../user-guide/mtc.html#hpo-mtc-filter-strategy"><span class="std std-ref">HPO MTC filter strategy</span></a> section for more info.</p>
 <p>We recommend creating an instance using the <a class="reference internal" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter" title="gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter"><code class="xref py py-func docutils literal notranslate"><span class="pre">default_filter()</span></code></a> static factory method.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO">
+<span class="sig-name descname"><span class="pre">NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='HMF02',</span> <span class="pre">reason='Skipping</span> <span class="pre">term</span> <span class="pre">because</span> <span class="pre">no</span> <span class="pre">genotype</span> <span class="pre">has</span> <span class="pre">more</span> <span class="pre">than</span> <span class="pre">one</span> <span class="pre">observed</span> <span class="pre">HPO</span> <span class="pre">count'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.SAME_COUNT_AS_THE_ONLY_CHILD">
+<span class="sig-name descname"><span class="pre">SAME_COUNT_AS_THE_ONLY_CHILD</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='HMF03',</span> <span class="pre">reason='Skipping</span> <span class="pre">term</span> <span class="pre">because</span> <span class="pre">of</span> <span class="pre">a</span> <span class="pre">child</span> <span class="pre">term</span> <span class="pre">with</span> <span class="pre">the</span> <span class="pre">same</span> <span class="pre">individual</span> <span class="pre">counts'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.SAME_COUNT_AS_THE_ONLY_CHILD" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SAME_OBSERVED_PROPORTIONS">
+<span class="sig-name descname"><span class="pre">SKIPPING_SAME_OBSERVED_PROPORTIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='HMF04',</span> <span class="pre">reason='Skipping</span> <span class="pre">term</span> <span class="pre">because</span> <span class="pre">all</span> <span class="pre">genotypes</span> <span class="pre">have</span> <span class="pre">same</span> <span class="pre">HPO</span> <span class="pre">observed</span> <span class="pre">proportions'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SAME_OBSERVED_PROPORTIONS" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS">
+<span class="sig-name descname"><span class="pre">SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='HMF05',</span> <span class="pre">reason='Skipping</span> <span class="pre">term</span> <span class="pre">because</span> <span class="pre">one</span> <span class="pre">genotype</span> <span class="pre">had</span> <span class="pre">zero</span> <span class="pre">observations'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_NON_PHENOTYPE_TERM">
+<span class="sig-name descname"><span class="pre">SKIPPING_NON_PHENOTYPE_TERM</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='HMF07',</span> <span class="pre">reason='Skipping</span> <span class="pre">non</span> <span class="pre">phenotype</span> <span class="pre">term'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_NON_PHENOTYPE_TERM" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_GENERAL_TERM">
+<span class="sig-name descname"><span class="pre">SKIPPING_GENERAL_TERM</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PhenotypeMtcResult(status=False,</span> <span class="pre">issue=PhenotypeMtcIssue(code='HMF08',</span> <span class="pre">reason='Skipping</span> <span class="pre">general</span> <span class="pre">term'))</span></em><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_GENERAL_TERM" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">default_filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo:</span> <span class="pre">~hpotk.ontology._api.MinimalOntology</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">term_frequency_threshold:</span> <span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phenotypic_abnormality:</span> <span class="pre">~hpotk.model._term_id.TermId</span> <span class="pre">=</span> <span class="pre">DefaultTermId(idx=2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value=HP:0000118)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#HpoMtcFilter.default_filter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter" title="Link to this definition"></a></dt>
@@ -293,6 +379,12 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.possible_results">
+<span class="sig-name descname"><span class="pre">possible_results</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Collection" title="(in Python v3.12)"><span class="pre">Collection</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#HpoMtcFilter.possible_results"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.possible_results" title="Link to this definition"></a></dt>
+<dd><p>Return all possible result types which the <cite>PhenotypeMtcFilter</cite> can produce.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.HpoMtcFilter.filter_method_name">
 <span class="sig-name descname"><span class="pre">filter_method_name</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#HpoMtcFilter.filter_method_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.HpoMtcFilter.filter_method_name" title="Link to this definition"></a></dt>
diff --git a/stable/apidocs/gpsea.analysis.pcats.html b/stable/apidocs/gpsea.analysis.pcats.html
index 6d5deef97..2cd98cc27 100644
--- a/stable/apidocs/gpsea.analysis.pcats.html
+++ b/stable/apidocs/gpsea.analysis.pcats.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pcats package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pcats package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -135,12 +134,6 @@
 <p><cite>MultiPhenotypeAnalysisResult</cite> reports the outcome of <a class="reference internal" href="#gpsea.analysis.pcats.MultiPhenotypeAnalysis" title="gpsea.analysis.pcats.MultiPhenotypeAnalysis"><code class="xref py py-class docutils literal notranslate"><span class="pre">MultiPhenotypeAnalysis</span></code></a>.</p>
 <p>The result consists of several arrays with items
 with the order determined by the phenotype order.</p>
-<dl class="py property">
-<dt class="sig sig-object py" id="gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.phenotypes">
-<em class="property"><span class="pre">abstract</span><span class="w"> </span><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">phenotypes</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><span class="pre">P</span><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.phenotypes" title="Link to this definition"></a></dt>
-<dd><p>Get the tested phenotypes.</p>
-</dd></dl>
-
 <dl class="py property">
 <dt class="sig sig-object py" id="gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.n_usable">
 <em class="property"><span class="pre">abstract</span><span class="w"> </span><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">n_usable</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.n_usable" title="Link to this definition"></a></dt>
@@ -187,26 +180,6 @@
 <dd><p>Get total count of tests that were run for this analysis.</p>
 </dd></dl>
 
-<dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.summarize">
-<span class="sig-name descname"><span class="pre">summarize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_phenotype_category</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.analysis.predicate.html#gpsea.analysis.predicate.PatientCategory" title="gpsea.analysis.predicate._api.PatientCategory"><span class="pre">PatientCategory</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://pandas.pydata.org/pandas-docs/version/2.0.0/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.0.0)"><span class="pre">DataFrame</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/pcats/_impl.html#MultiPhenotypeAnalysisResult.summarize"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.summarize" title="Link to this definition"></a></dt>
-<dd><p>Create a data frame with summary of the genotype phenotype analysis.</p>
-<p>The <em>rows</em> of the frame correspond to the analyzed HPO terms.</p>
-<p>The columns of the data frame have <cite>Count</cite> and <cite>Percentage</cite> per used genotype predicate.</p>
-<p><strong>Example</strong></p>
-<p>If we use <code class="xref py py-class docutils literal notranslate"><span class="pre">VariantEffectPredicate</span></code>
-which can compare phenotype with and without a missense variant, we will have a data frame
-that looks like this:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>MISSENSE_VARIANT on `NM_1234.5`                       No                  Yes
-                                                      Count    Percent    Count    Percent   Corrected p value  p value
-Arachnodactyly [HP:0001166]                           1/10         10%    13/16        81%   0.020299           0.000781
-Abnormality of the musculature [HP:0003011]           6/6         100%    11/11       100%   1.000000           1.000000
-Abnormal nervous system physiology [HP:0012638]       9/9         100%    15/15       100%   1.000000           1.000000
-...                                                   ...      ...        ...      ...       ...                ...
-</pre></div>
-</div>
-</dd></dl>
-
 </dd></dl>
 
 <dl class="py class">
@@ -228,7 +201,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.analysis.pcats.HpoTermAnalysisResult">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.pcats.</span></span><span class="sig-name descname"><span class="pre">HpoTermAnalysisResult</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">phenotypes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_usable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_counts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://pandas.pydata.org/pandas-docs/version/2.0.0/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.0.0)"><span class="pre">DataFrame</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pvals</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">corrected_pvals</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">gt_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtc_filter_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtc_filter_results</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtc_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/pcats/_impl.html#HpoTermAnalysisResult"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.pcats.HpoTermAnalysisResult" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.pcats.</span></span><span class="sig-name descname"><span class="pre">HpoTermAnalysisResult</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pheno_predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypePolyPredicate"><span class="pre">PhenotypePolyPredicate</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_usable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_counts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://pandas.pydata.org/pandas-docs/version/2.0.0/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.0.0)"><span class="pre">DataFrame</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pvals</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">corrected_pvals</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">gt_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtc_filter_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtc_filter_results</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcResult"><span class="pre">PhenotypeMtcResult</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtc_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/pcats/_impl.html#HpoTermAnalysisResult"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.pcats.HpoTermAnalysisResult" title="Link to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">BaseMultiPhenotypeAnalysisResult</span></code>[<a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><code class="xref py py-class docutils literal notranslate"><span class="pre">TermId</span></code></a>]</p>
 <p><cite>HpoTermAnalysisResult</cite> includes the <a class="reference internal" href="#gpsea.analysis.pcats.HpoTermAnalysis" title="gpsea.analysis.pcats.HpoTermAnalysis"><code class="xref py py-class docutils literal notranslate"><span class="pre">HpoTermAnalysis</span></code></a> results.</p>
 <p>On top of the attributes of <a class="reference internal" href="#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult" title="gpsea.analysis.pcats.MultiPhenotypeAnalysisResult"><code class="xref py py-class docutils literal notranslate"><span class="pre">MultiPhenotypeAnalysisResult</span></code></a> parent,
diff --git a/stable/apidocs/gpsea.analysis.pcats.stats.html b/stable/apidocs/gpsea.analysis.pcats.stats.html
index b4b46aa4e..361f21c85 100644
--- a/stable/apidocs/gpsea.analysis.pcats.stats.html
+++ b/stable/apidocs/gpsea.analysis.pcats.stats.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pcats.stats package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pcats.stats package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/stable/apidocs/gpsea.analysis.predicate.genotype.html b/stable/apidocs/gpsea.analysis.predicate.genotype.html
index 6a57b572b..0988daa0d 100644
--- a/stable/apidocs/gpsea.analysis.predicate.genotype.html
+++ b/stable/apidocs/gpsea.analysis.predicate.genotype.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.genotype package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.genotype package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,11 +17,13 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../_static/copybutton.js?v=6dbb43f8"></script>
+        <script>window.MathJax = {"TeX": {"Macros": {"RR": "{\\mathbb{R}}"}}}</script>
+        <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -41,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -111,20 +112,13 @@
 that test the genotype axis.</p>
 </dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.boolean_predicate">
-<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">boolean_predicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#boolean_predicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.boolean_predicate" title="Link to this definition"></a></dt>
-<dd><p>Create a genotype boolean predicate from given <cite>variant_predicate</cite>
-to test for presence of at least one matching allele in the patient.</p>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.groups_predicate">
 <span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">groups_predicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">group_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#groups_predicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.groups_predicate" title="Link to this definition"></a></dt>
 <dd><p>Create a genotype predicate that bins the patient into one of <em>n</em> groups.</p>
 <p>The genotype groups <em>should</em> not overlap.
 In case of an overlap, the patient will be assigned into no group (<cite>None</cite>).</p>
-<p>See the <a class="reference internal" href="../user-guide/predicates.html#groups-predicate"><span class="std std-ref">Groups predicate</span></a> section for an example.</p>
+<p>See the <a class="reference internal" href="../user-guide/predicates/groups_predicate.html#groups-predicate"><span class="std std-ref">Groups Predicate</span></a> section for an example.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -135,32 +129,11 @@
 </dl>
 </dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.filtering_predicate">
-<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">filtering_predicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">targets</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Collection" title="(in Python v3.12)"><span class="pre">Collection</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.analysis.predicate.html#gpsea.analysis.predicate.Categorization" title="gpsea.analysis.predicate._api.Categorization"><span class="pre">Categorization</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#filtering_predicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.filtering_predicate" title="Link to this definition"></a></dt>
-<dd><p>Filtering predicate applies the base <cite>predicate</cite> but only returns the categorizations
-from the provided <cite>targets</cite> collection.</p>
-<p>This can be useful if only some of the categorizations are interesting.
-For instance, if we only seek to compare the differences between heterozygous and hemizygous variants,
-but the predicate also bins the patients into homozygous reference, and biallelic alt genotype groups.</p>
-<p>See the <a class="reference internal" href="../user-guide/predicates.html#filtering-predicate"><span class="std std-ref">Filtering predicate</span></a> section for an example.</p>
-<p>The <cite>predicate</cite> is checked for being able to produce the all items in <cite>targets</cite>
-and the <cite>targets</cite> must include at least 2 categorizations.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>predicate</strong> – the base predicate whose categorizations are subject to filteration.</p></li>
-<li><p><strong>targets</strong> – the categorizations to retain</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.sex_predicate">
 <span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">sex_predicate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#sex_predicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.sex_predicate" title="Link to this definition"></a></dt>
 <dd><p>Get a genotype predicate for categorizing patients by their <a class="reference internal" href="gpsea.model.html#gpsea.model.Sex" title="gpsea.model.Sex"><code class="xref py py-class docutils literal notranslate"><span class="pre">Sex</span></code></a>.</p>
-<p>See the <a class="reference internal" href="../user-guide/predicates.html#sex-predicate"><span class="std std-ref">Partition by the sex of the individual</span></a> section for an example.</p>
+<p>See the <a class="reference internal" href="../user-guide/predicates/male_female_predicate.html#male-female-predicate"><span class="std std-ref">Partition by the sex of the individual</span></a> section for an example.</p>
 </dd></dl>
 
 <dl class="py function">
@@ -170,7 +143,7 @@
 as listed in <a class="reference internal" href="gpsea.model.html#gpsea.model.Patient.diseases" title="gpsea.model.Patient.diseases"><code class="xref py py-attr docutils literal notranslate"><span class="pre">diseases</span></code></a> attribute.</p>
 <p>If an individual is diagnosed with more than one disease from the provided <cite>diagnoses</cite>,
 the individual will be assigned into no group (<cite>None</cite>).</p>
-<p>See the <a class="reference internal" href="../user-guide/predicates.html#diagnosis-predicate"><span class="std std-ref">Partition by a diagnosis</span></a> section for an example.</p>
+<p>See the <a class="reference internal" href="../user-guide/predicates/diagnosis_predicate.html#diagnosis-predicate"><span class="std std-ref">Partition by a diagnosis</span></a> section for an example.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -183,59 +156,141 @@
 </dl>
 </dd></dl>
 
-<dl class="py class">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">ModeOfInheritancePredicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">allele_counter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.AlleleCounter" title="gpsea.analysis.predicate.genotype._counter.AlleleCounter"><span class="pre">AlleleCounter</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode_of_inheritance_info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ModeOfInheritanceInfo</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="Link to this definition"></a></dt>
-<dd><p>Bases: <a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a></p>
-<p><cite>ModeOfInheritancePredicate</cite> assigns an individual into a group based on compatibility with
-the selected mode of inheritance.</p>
-<dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">autosomal_dominant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype._gt_predicates.ModeOfInheritancePredicate"><span class="pre">ModeOfInheritancePredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.autosomal_dominant"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant" title="Link to this definition"></a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.autosomal_dominant">
+<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">autosomal_dominant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#autosomal_dominant"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.autosomal_dominant" title="Link to this definition"></a></dt>
 <dd><p>Create a predicate that assigns the patient either
 into homozygous reference or heterozygous
 group in line with the autosomal dominant mode of inheritance.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing.</p>
+<dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing
+or <cite>None</cite> if all variants should be used.</p>
 </dd>
 </dl>
 </dd></dl>
 
-<dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">autosomal_recessive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype._gt_predicates.ModeOfInheritancePredicate"><span class="pre">ModeOfInheritancePredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.autosomal_recessive"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive" title="Link to this definition"></a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.autosomal_recessive">
+<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">autosomal_recessive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#autosomal_recessive"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.autosomal_recessive" title="Link to this definition"></a></dt>
 <dd><p>Create a predicate that assigns the patient either into
 homozygous reference, heterozygous, or biallelic alternative allele
 (homozygous alternative or compound heterozygous)
 group in line with the autosomal recessive mode of inheritance.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing.</p>
+<dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing
+or <cite>None</cite> if all variants should be used</p>
 </dd>
 </dl>
 </dd></dl>
 
-<dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">x_dominant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype._gt_predicates.ModeOfInheritancePredicate"><span class="pre">ModeOfInheritancePredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.x_dominant"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant" title="Link to this definition"></a></dt>
-<dd><p>Create a predicate that assigns the patient either into
-homozygous reference or heterozygous
-group in line with the X-linked dominant mode of inheritance.</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.monoallelic_predicate">
+<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">monoallelic_predicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">b_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">('A',</span> <span class="pre">'B')</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#monoallelic_predicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.monoallelic_predicate" title="Link to this definition"></a></dt>
+<dd><p>The predicate bins patient into one of two groups, <cite>A</cite> and <cite>B</cite>,
+based on presence of <em>exactly</em> one allele of a variant
+that meets the predicate criteria.</p>
+<p>The number of alleles <span class="math notranslate nohighlight">\(count_{A}\)</span> and <span class="math notranslate nohighlight">\(count_{B}\)</span>
+is computed using <cite>a_predicate</cite> and <cite>b_predicate</cite>
+and the individual is assigned into a group
+based on the following table:</p>
+<table class="docutils align-default">
+<thead>
+<tr class="row-odd"><th class="head"><p>Group</p></th>
+<th class="head"><p><span class="math notranslate nohighlight">\(count_{A}\)</span></p></th>
+<th class="head"><p><span class="math notranslate nohighlight">\(count_{B}\)</span></p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>A</p></td>
+<td><p>1</p></td>
+<td><p>0</p></td>
+</tr>
+<tr class="row-odd"><td><p>B</p></td>
+<td><p>0</p></td>
+<td><p>1</p></td>
+</tr>
+</tbody>
+</table>
+<p>The individuals with different allele counts
+(e.g. <span class="math notranslate nohighlight">\(count_{A} = 0\)</span> and <span class="math notranslate nohighlight">\(count_{B} = 2\)</span>)
+are assigned into the <code class="docutils literal notranslate"><span class="pre">None</span></code> group and, thus, omitted from the analysis.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing.</p>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>a_predicate</strong> – predicate to test if the variants
+meet the criteria of the first group (named <cite>A</cite> by default).</p></li>
+<li><p><strong>b_predicate</strong> – predicate to test if the variants
+meet the criteria of the second group (named <cite>B</cite> by default).</p></li>
+<li><p><strong>names</strong> – group names (default <code class="docutils literal notranslate"><span class="pre">('A',</span> <span class="pre">'B')</span></code>).</p></li>
+</ul>
 </dd>
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.biallelic_predicate">
+<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">biallelic_predicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">b_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">('A',</span> <span class="pre">'B')</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#biallelic_predicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.biallelic_predicate" title="Link to this definition"></a></dt>
+<dd><p>The predicate bins patient into one of the three groups,
+<cite>AA</cite>, <cite>AB</cite>, and <cite>BB</cite>,
+based on presence of one or two variant alleles
+that meet the predicate criteria.</p>
+<p>The number of alleles <span class="math notranslate nohighlight">\(count_{A}\)</span> and <span class="math notranslate nohighlight">\(count_{B}\)</span>
+is computed using <cite>a_predicate</cite> and <cite>b_predicate</cite>
+and the individual is assigned into a group
+based on the following table:</p>
+<table class="docutils align-default">
+<thead>
+<tr class="row-odd"><th class="head"><p>Group</p></th>
+<th class="head"><p><span class="math notranslate nohighlight">\(count_{A}\)</span></p></th>
+<th class="head"><p><span class="math notranslate nohighlight">\(count_{B}\)</span></p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>AA</p></td>
+<td><p>2</p></td>
+<td><p>0</p></td>
+</tr>
+<tr class="row-odd"><td><p>AB</p></td>
+<td><p>1</p></td>
+<td><p>1</p></td>
+</tr>
+<tr class="row-even"><td><p>AA</p></td>
+<td><p>0</p></td>
+<td><p>2</p></td>
+</tr>
+</tbody>
+</table>
+<p>The individuals with different allele counts
+(e.g. <span class="math notranslate nohighlight">\(count_{A} = 1\)</span> and <span class="math notranslate nohighlight">\(count_{B} = 2\)</span>)
+are assigned into the <code class="docutils literal notranslate"><span class="pre">None</span></code> group and will be, thus,
+omitted from the analysis.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>a_predicate</strong> – predicate to test if the variants
+meet the criteria of the first group (named <cite>A</cite> by default).</p></li>
+<li><p><strong>b_predicate</strong> – predicate to test if the variants
+meet the criteria of the second group (named <cite>B</cite> by default).</p></li>
+<li><p><strong>names</strong> – group names (default <code class="docutils literal notranslate"><span class="pre">('A',</span> <span class="pre">'B')</span></code>).</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.genotype.</span></span><span class="sig-name descname"><span class="pre">ModeOfInheritancePredicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">allele_counter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.AlleleCounter" title="gpsea.analysis.predicate.genotype._counter.AlleleCounter"><span class="pre">AlleleCounter</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode_of_inheritance_info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ModeOfInheritanceInfo</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="Link to this definition"></a></dt>
+<dd><p>Bases: <a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a></p>
+<p><cite>ModeOfInheritancePredicate</cite> assigns an individual into a group based on compatibility with
+the selected mode of inheritance.</p>
 <dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">x_recessive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype._gt_predicates.ModeOfInheritancePredicate"><span class="pre">ModeOfInheritancePredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.x_recessive"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive" title="Link to this definition"></a></dt>
-<dd><p>Create a predicate that assigns the patient either into
-homozygous reference, heterozygous, biallelic alternative allele
-(homozygous alternative or compound heterozygous), or hemizygous
-group in line with the X-linked recessive mode of inheritance.</p>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">autosomal_dominant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.autosomal_dominant"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant" title="Link to this definition"></a></dt>
+<dd><p>Create a predicate that assigns the patient either
+into homozygous reference or heterozygous
+group in line with the autosomal dominant mode of inheritance.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing.</p>
@@ -244,9 +299,17 @@
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.from_moi_info">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_moi_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode_of_inheritance_data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ModeOfInheritanceInfo</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype._gt_predicates.ModeOfInheritancePredicate"><span class="pre">ModeOfInheritancePredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.from_moi_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.from_moi_info" title="Link to this definition"></a></dt>
-<dd><p>Create a predicate for specified mode of inheritance data.</p>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">autosomal_recessive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_predicate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype._api.GenotypePolyPredicate"><span class="pre">GenotypePolyPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_gt_predicates.html#ModeOfInheritancePredicate.autosomal_recessive"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive" title="Link to this definition"></a></dt>
+<dd><p>Create a predicate that assigns the patient either into
+homozygous reference, heterozygous, or biallelic alternative allele
+(homozygous alternative or compound heterozygous)
+group in line with the autosomal recessive mode of inheritance.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>variant_predicate</strong> – a predicate for choosing the variants for testing.</p>
+</dd>
+</dl>
 </dd></dl>
 
 <dl class="py method">
@@ -350,6 +413,13 @@
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p><cite>VariantPredicates</cite> is a static utility class to provide the variant predicates
 that are relatively simple to configure.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.VariantPredicates.true">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">true</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_variant.html#VariantPredicates.true"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.VariantPredicates.true" title="Link to this definition"></a></dt>
+<dd><p>Prepare an absolutely inclusive <a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> - a predicate that returns <cite>True</cite>
+for any variant whatsoever.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.VariantPredicates.all">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_variant.html#VariantPredicates.all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.VariantPredicates.all" title="Link to this definition"></a></dt>
@@ -460,6 +530,21 @@
 <dt class="sig sig-object py" id="gpsea.analysis.predicate.genotype.VariantPredicates.exon">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">exon</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">exon</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tx_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype._api.VariantPredicate"><span class="pre">VariantPredicate</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/genotype/_variant.html#VariantPredicates.exon"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.genotype.VariantPredicates.exon" title="Link to this definition"></a></dt>
 <dd><p>Prepare a <a class="reference internal" href="#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> that tests if the variant overlaps with an exon of a specific transcript.</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>We use 1-based numbering to number the exons,
+not the usual 0-based numbering of the computer science.
+Therefore, the first exon of the transcript
+has <code class="docutils literal notranslate"><span class="pre">exon_number==1</span></code>, the second exon is <code class="docutils literal notranslate"><span class="pre">2</span></code>, and so on …</p>
+</div>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>We do not check if the <cite>exon_number</cite> spans
+beyond the number of exons of the given <cite>transcript_id</cite>!
+Therefore, <code class="docutils literal notranslate"><span class="pre">exon_number==10,000</span></code> will effectively return <cite>False</cite>
+for <em>all</em> variants!!! 😱
+Well, at least the genome variants of the <em>Homo sapiens sapiens</em> taxon…</p>
+</div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
diff --git a/stable/apidocs/gpsea.analysis.predicate.html b/stable/apidocs/gpsea.analysis.predicate.html
index 9e46018f0..bda3881be 100644
--- a/stable/apidocs/gpsea.analysis.predicate.html
+++ b/stable/apidocs/gpsea.analysis.predicate.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,11 +17,13 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../_static/copybutton.js?v=6dbb43f8"></script>
+        <script>window.MathJax = {"TeX": {"Macros": {"RR": "{\\mathbb{R}}"}}}</script>
+        <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -41,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +62,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -256,11 +257,13 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html">gpsea.analysis.predicate.genotype package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate"><code class="docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.boolean_predicate"><code class="docutils literal notranslate"><span class="pre">boolean_predicate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.groups_predicate"><code class="docutils literal notranslate"><span class="pre">groups_predicate()</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.filtering_predicate"><code class="docutils literal notranslate"><span class="pre">filtering_predicate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.sex_predicate"><code class="docutils literal notranslate"><span class="pre">sex_predicate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.diagnosis_predicate"><code class="docutils literal notranslate"><span class="pre">diagnosis_predicate()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_dominant"><code class="docutils literal notranslate"><span class="pre">autosomal_dominant()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_recessive"><code class="docutils literal notranslate"><span class="pre">autosomal_recessive()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.monoallelic_predicate"><code class="docutils literal notranslate"><span class="pre">monoallelic_predicate()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.biallelic_predicate"><code class="docutils literal notranslate"><span class="pre">biallelic_predicate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate"><code class="docutils literal notranslate"><span class="pre">ModeOfInheritancePredicate</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.AlleleCounter"><code class="docutils literal notranslate"><span class="pre">AlleleCounter</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate"><code class="docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a></li>
@@ -270,7 +273,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 </li>
 <li class="toctree-l1"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html">gpsea.analysis.predicate.phenotype package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate"><code class="docutils literal notranslate"><span class="pre">PhenotypePolyPredicate</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate"><code class="docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate"><code class="docutils literal notranslate"><span class="pre">HpoPredicate</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate"><code class="docutils literal notranslate"><span class="pre">DiseasePresencePredicate</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypeCategorization"><code class="docutils literal notranslate"><span class="pre">PhenotypeCategorization</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest"><code class="docutils literal notranslate"><span class="pre">prepare_predicates_for_terms_of_interest()</span></code></a></li>
diff --git a/stable/apidocs/gpsea.analysis.predicate.phenotype.html b/stable/apidocs/gpsea.analysis.predicate.phenotype.html
index 6440d663e..76c58386b 100644
--- a/stable/apidocs/gpsea.analysis.predicate.phenotype.html
+++ b/stable/apidocs/gpsea.analysis.predicate.phenotype.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.predicate.phenotype package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.predicate.phenotype package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -106,7 +105,7 @@
 <p>The <cite>gpsea.analysis.predicate.phenotype</cite> package provides the <a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhenotypePolyPredicate</span></code></a>
 for assigning <a class="reference internal" href="gpsea.model.html#gpsea.model.Patient" title="gpsea.model.Patient"><code class="xref py py-class docutils literal notranslate"><span class="pre">Patient</span></code></a> into a phenotype group.</p>
 <p>An individual can be assigned based on presence/absence of a disease diagnosis (<a class="reference internal" href="#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate" title="gpsea.analysis.predicate.phenotype.DiseasePresencePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">DiseasePresencePredicate</span></code></a>)
-or using the phenotype features encoded into HPO terms (<a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate" title="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code></a>).</p>
+or using the phenotype features encoded into HPO terms (<code class="xref py py-class docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code>).</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.phenotype.</span></span><span class="sig-name descname"><span class="pre">PhenotypePolyPredicate</span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#PhenotypePolyPredicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="Link to this definition"></a></dt>
@@ -139,47 +138,48 @@
 </dd></dl>
 
 <dl class="py class">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.phenotype.</span></span><span class="sig-name descname"><span class="pre">PropagatingPhenotypePredicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">query</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_implies_phenotype_excluded</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#PropagatingPhenotypePredicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.HpoPredicate">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.phenotype.</span></span><span class="sig-name descname"><span class="pre">HpoPredicate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">query</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_implies_phenotype_excluded</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#HpoPredicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.HpoPredicate" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhenotypePolyPredicate</span></code></a>[<a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><code class="xref py py-class docutils literal notranslate"><span class="pre">TermId</span></code></a>]</p>
-<p><cite>PropagatingPhenotypePredicate</cite> tests if a patient is annotated with an HPO term.</p>
+<p><cite>HpoPredicate</cite> tests if a patient is annotated with an HPO term.</p>
 <p>Note, <cite>query</cite> must be a term of the provided <cite>hpo</cite>!</p>
+<p>See <a class="reference internal" href="../user-guide/predicates/hpo_predicate.html#hpo-predicate"><span class="std std-ref">HPO predicate</span></a> section for an example usage.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>hpo</strong> – HPO object</p></li>
+<li><p><strong>hpo</strong> – HPO ontology</p></li>
 <li><p><strong>query</strong> – the HPO term to test</p></li>
 <li><p><strong>missing_implies_phenotype_excluded</strong> – <cite>True</cite> if lack of an explicit annotation implies term’s absence`.</p></li>
 </ul>
 </dd>
 </dl>
 <dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_question_base">
-<span class="sig-name descname"><span class="pre">get_question_base</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#PropagatingPhenotypePredicate.get_question_base"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_question_base" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.HpoPredicate.get_question_base">
+<span class="sig-name descname"><span class="pre">get_question_base</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#HpoPredicate.get_question_base"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.HpoPredicate.get_question_base" title="Link to this definition"></a></dt>
 <dd><p>Prepare a <cite>str</cite> with the question the predicate can answer.</p>
 </dd></dl>
 
 <dl class="py property">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.phenotype">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">phenotype</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a></em><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.phenotype" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.HpoPredicate.phenotype">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">phenotype</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a></em><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.HpoPredicate.phenotype" title="Link to this definition"></a></dt>
 <dd><p>Get the phenotype entity of interest.</p>
 </dd></dl>
 
 <dl class="py property">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.present_phenotype_categorization">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">present_phenotype_categorization</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypeCategorization" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypeCategorization"><span class="pre">PhenotypeCategorization</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.present_phenotype_categorization" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.HpoPredicate.present_phenotype_categorization">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">present_phenotype_categorization</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypeCategorization" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypeCategorization"><span class="pre">PhenotypeCategorization</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.HpoPredicate.present_phenotype_categorization" title="Link to this definition"></a></dt>
 <dd><p>Get the categorization which represents the group of the patients who exibit the investigated phenotype.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_categorizations">
-<span class="sig-name descname"><span class="pre">get_categorizations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypeCategorization" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypeCategorization"><span class="pre">PhenotypeCategorization</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#PropagatingPhenotypePredicate.get_categorizations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_categorizations" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.HpoPredicate.get_categorizations">
+<span class="sig-name descname"><span class="pre">get_categorizations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypeCategorization" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypeCategorization"><span class="pre">PhenotypeCategorization</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#HpoPredicate.get_categorizations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.HpoPredicate.get_categorizations" title="Link to this definition"></a></dt>
 <dd><p>Get a sequence of all categories which the <cite>PolyPredicate</cite> can produce.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.test">
-<span class="sig-name descname"><span class="pre">test</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">patient</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.model.html#gpsea.model.Patient" title="gpsea.model._cohort.Patient"><span class="pre">Patient</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypeCategorization" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypeCategorization"><span class="pre">PhenotypeCategorization</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#PropagatingPhenotypePredicate.test"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.test" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.HpoPredicate.test">
+<span class="sig-name descname"><span class="pre">test</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">patient</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.model.html#gpsea.model.Patient" title="gpsea.model._cohort.Patient"><span class="pre">Patient</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypeCategorization" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypeCategorization"><span class="pre">PhenotypeCategorization</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_pheno.html#HpoPredicate.test"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.HpoPredicate.test" title="Link to this definition"></a></dt>
 <dd><p>An HPO TermID is given when initializing the class.
 Given a Patient class, this function tests whether the patient has the
 given phenotype.</p>
@@ -284,7 +284,7 @@
 <dl class="py function">
 <dt class="sig sig-object py" id="gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest">
 <span class="sig-prename descclassname"><span class="pre">gpsea.analysis.predicate.phenotype.</span></span><span class="sig-name descname"><span class="pre">prepare_predicates_for_terms_of_interest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cohort</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="gpsea.model.html#gpsea.model.Patient" title="gpsea.model._cohort.Patient"><span class="pre">Patient</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.graph.html#hpotk.graph.GraphAware" title="(in hpo-toolkit)"><span class="pre">GraphAware</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_implies_excluded</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_n_of_patients_with_term</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype._pheno.PhenotypePolyPredicate"><span class="pre">PhenotypePolyPredicate</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/gpsea/analysis/predicate/phenotype/_util.html#prepare_predicates_for_terms_of_interest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest" title="Link to this definition"></a></dt>
-<dd><p>A convenience method for creating a battery of <a class="reference internal" href="#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate" title="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code></a> predicates
+<dd><p>A convenience method for creating a battery of <code class="xref py py-class docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code> predicates
 for testing all phenotypes of interest.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/stable/apidocs/gpsea.analysis.pscore.html b/stable/apidocs/gpsea.analysis.pscore.html
index 4826fa8a2..490bbf579 100644
--- a/stable/apidocs/gpsea.analysis.pscore.html
+++ b/stable/apidocs/gpsea.analysis.pscore.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pscore package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pscore package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/stable/apidocs/gpsea.analysis.pscore.stats.html b/stable/apidocs/gpsea.analysis.pscore.stats.html
index e7ef51577..b6b5fd92e 100644
--- a/stable/apidocs/gpsea.analysis.pscore.stats.html
+++ b/stable/apidocs/gpsea.analysis.pscore.stats.html
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   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.analysis.pscore.stats package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.analysis.pscore.stats package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
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         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
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     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="gpsea.data package" href="gpsea.data.html" />
+    <link rel="next" title="gpsea.model package" href="gpsea.model.html" />
     <link rel="prev" title="gpsea.analysis.pscore package" href="gpsea.analysis.pscore.html" /> 
 </head>
 
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
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@@ -60,7 +60,6 @@
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 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -153,7 +152,7 @@
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="gpsea.analysis.pscore.html" class="btn btn-neutral float-left" title="gpsea.analysis.pscore package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="gpsea.data.html" class="btn btn-neutral float-right" title="gpsea.data package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="gpsea.model.html" class="btn btn-neutral float-right" title="gpsea.model package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/stable/apidocs/gpsea.config.html b/stable/apidocs/gpsea.config.html
index efcebe05c..5258bc20a 100644
--- a/stable/apidocs/gpsea.config.html
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@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.config module &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.config module &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
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         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
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         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
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-                0.3
+                0.4
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 <div role="search">
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diff --git a/stable/apidocs/gpsea.data.html b/stable/apidocs/gpsea.data.html
deleted file mode 100644
index deda4e185..000000000
--- a/stable/apidocs/gpsea.data.html
+++ /dev/null
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-  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.data package &mdash; GPSEA 0.3.0 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
-      <link rel="stylesheet" type="text/css" href="../_static/gpsea.css?v=547657ed" />
-
-  
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-    <script src="../_static/js/html5shiv.min.js"></script>
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-        <script src="../_static/copybutton.js?v=6dbb43f8"></script>
-    <script src="../_static/js/theme.js"></script>
-    <link rel="index" title="Index" href="../genindex.html" />
-    <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="gpsea.model package" href="gpsea.model.html" />
-    <link rel="prev" title="gpsea.analysis.pscore.stats package" href="gpsea.analysis.pscore.stats.html" /> 
-</head>
-
-<body class="wy-body-for-nav"> 
-  <div class="wy-grid-for-nav">
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-scroll">
-        <div class="wy-side-nav-search" >
-
-          
-          
-          <a href="../index.html" class="icon icon-home">
-            GPSEA
-          </a>
-              <div class="version">
-                0.3
-              </div>
-<div role="search">
-  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
-    <input type="hidden" name="area" value="default" />
-  </form>
-</div>
-        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Installation &amp; Tutorial</span></p>
-<ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../user-guide/index.html">User guide</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="modules.html">API reference</a><ul class="current">
-<li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
-<li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
-<li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4 current"><a class="current reference internal" href="#">gpsea.data package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="gpsea.html#submodules">Submodules</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-        </div>
-      </div>
-    </nav>
-
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
-          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../index.html">GPSEA</a>
-      </nav>
-
-      <div class="wy-nav-content">
-        <div class="rst-content">
-          <div role="navigation" aria-label="Page navigation">
-  <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="modules.html">API reference</a></li>
-          <li class="breadcrumb-item"><a href="gpsea.html">gpsea package</a></li>
-      <li class="breadcrumb-item active">gpsea.data package</li>
-      <li class="wy-breadcrumbs-aside">
-            <a href="../_sources/apidocs/gpsea.data.rst.txt" rel="nofollow"> View page source</a>
-      </li>
-  </ul>
-  <hr/>
-</div>
-          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
-           <div itemprop="articleBody">
-             
-  <section id="module-gpsea.data">
-<span id="gpsea-data-package"></span><h1>gpsea.data package<a class="headerlink" href="#module-gpsea.data" title="Link to this heading"></a></h1>
-<dl class="py function">
-<dt class="sig sig-object py" id="gpsea.data.get_toy_cohort">
-<span class="sig-prename descclassname"><span class="pre">gpsea.data.</span></span><span class="sig-name descname"><span class="pre">get_toy_cohort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="gpsea.model.html#gpsea.model.Cohort" title="gpsea.model._cohort.Cohort"><span class="pre">Cohort</span></a></span></span><a class="reference internal" href="../_modules/gpsea/data/_toy.html#get_toy_cohort"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.data.get_toy_cohort" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-</section>
-
-
-           </div>
-          </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="gpsea.analysis.pscore.stats.html" class="btn btn-neutral float-left" title="gpsea.analysis.pscore.stats package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="gpsea.model.html" class="btn btn-neutral float-right" title="gpsea.model package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>&#169; Copyright 2024.</p>
-  </div>
-
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
-    provided by <a href="https://readthedocs.org">Read the Docs</a>.
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-</footer>
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\ No newline at end of file
diff --git a/stable/apidocs/gpsea.html b/stable/apidocs/gpsea.html
index c43bbb07f..4dc05eebb 100644
--- a/stable/apidocs/gpsea.html
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   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
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         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -43,7 +43,7 @@
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+                0.4
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 <div role="search">
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@@ -62,7 +62,6 @@
 <li class="toctree-l2 current"><a class="current reference internal" href="#">gpsea package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#subpackages">Subpackages</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -115,10 +114,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l2"><a class="reference internal" href="gpsea.analysis.html#subpackages">Subpackages</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="gpsea.data.html#gpsea.data.get_toy_cohort"><code class="docutils literal notranslate"><span class="pre">get_toy_cohort()</span></code></a></li>
-</ul>
-</li>
 <li class="toctree-l1"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.model.html#gpsea.model.Cohort"><code class="docutils literal notranslate"><span class="pre">Cohort</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.model.html#gpsea.model.Patient"><code class="docutils literal notranslate"><span class="pre">Patient</span></code></a></li>
@@ -184,12 +179,14 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.CohortVariantViewer"><code class="docutils literal notranslate"><span class="pre">CohortVariantViewer</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.CohortViewable"><code class="docutils literal notranslate"><span class="pre">CohortViewable</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.ProteinVisualizer"><code class="docutils literal notranslate"><span class="pre">ProteinVisualizer</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.ProteinVisualizable"><code class="docutils literal notranslate"><span class="pre">ProteinVisualizable</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.ProteinViewable"><code class="docutils literal notranslate"><span class="pre">ProteinViewable</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.DiseaseViewable"><code class="docutils literal notranslate"><span class="pre">DiseaseViewable</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.MtcStatsViewer"><code class="docutils literal notranslate"><span class="pre">MtcStatsViewer</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.summarize_hpo_analysis"><code class="docutils literal notranslate"><span class="pre">summarize_hpo_analysis()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="gpsea.view.html#gpsea.view.VariantTranscriptVisualizer"><code class="docutils literal notranslate"><span class="pre">VariantTranscriptVisualizer</span></code></a></li>
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 </ul>
diff --git a/stable/apidocs/gpsea.io.html b/stable/apidocs/gpsea.io.html
index 1a29d2e90..e79f4001d 100644
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   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.io module &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.io module &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
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-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
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@@ -40,7 +40,7 @@
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diff --git a/stable/apidocs/gpsea.model.genome.html b/stable/apidocs/gpsea.model.genome.html
index f7a7a5efa..18310348e 100644
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model.genome package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model.genome package &mdash; GPSEA 0.4.0 documentation</title>
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       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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@@ -17,7 +17,7 @@
   
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-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
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@@ -41,7 +41,7 @@
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+                0.4
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 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4 current"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
diff --git a/stable/apidocs/gpsea.model.html b/stable/apidocs/gpsea.model.html
index 67766d02c..2f14c8f9f 100644
--- a/stable/apidocs/gpsea.model.html
+++ b/stable/apidocs/gpsea.model.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.model package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.model package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -26,7 +26,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="gpsea.model.genome package" href="gpsea.model.genome.html" />
-    <link rel="prev" title="gpsea.data package" href="gpsea.data.html" /> 
+    <link rel="prev" title="gpsea.analysis.pscore.stats package" href="gpsea.analysis.pscore.stats.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4 current"><a class="current reference internal" href="#">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -1237,7 +1236,7 @@
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="gpsea.model.VariantEffect.NMD_TRANSCRIPT_VARIANT">
-<span class="sig-name descname"><span class="pre">NMD_TRANSCRIPT_VARIANT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('SO:0001621',)</span></em><a class="headerlink" href="#gpsea.model.VariantEffect.NMD_TRANSCRIPT_VARIANT" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">NMD_TRANSCRIPT_VARIANT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'SO:0001621'</span></em><a class="headerlink" href="#gpsea.model.VariantEffect.NMD_TRANSCRIPT_VARIANT" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py attribute">
@@ -1305,6 +1304,45 @@
 <span class="sig-name descname"><span class="pre">SEQUENCE_VARIANT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'SO:0001060'</span></em><a class="headerlink" href="#gpsea.model.VariantEffect.SEQUENCE_VARIANT" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.model.VariantEffect.to_display">
+<span class="sig-name descname"><span class="pre">to_display</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/model/_variant_effects.html#VariantEffect.to_display"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.model.VariantEffect.to_display" title="Link to this definition"></a></dt>
+<dd><p>Get a concise name of the variant effect that is suitable for showing to humans.</p>
+<p class="rubric">Example</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="o">.</span><span class="n">to_display</span><span class="p">()</span>
+<span class="go">&#39;missense&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_5TH_BASE_VARIANT</span><span class="o">.</span><span class="n">to_display</span><span class="p">()</span>
+<span class="go">&#39;splice donor 5th base&#39;</span>
+</pre></div>
+</div>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>a <cite>str</cite> with the name or <cite>‘n/a’</cite> if the variant effect was not assigned a concise name.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.model.VariantEffect.structural_so_id_to_display">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structural_so_id_to_display</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">so_term</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/model/_variant_effects.html#VariantEffect.structural_so_id_to_display"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.model.VariantEffect.structural_so_id_to_display" title="Link to this definition"></a></dt>
+<dd><p>Get a <cite>str</cite> with a concise name for representing a Sequence Ontology (SO) term identifier.</p>
+<p class="rubric">Example</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">structural_so_id_to_display</span><span class="p">(</span><span class="s1">&#39;SO:1000029&#39;</span><span class="p">)</span>
+<span class="go">&#39;chromosomal deletion&#39;</span>
+</pre></div>
+</div>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>so_term</strong> – a CURIE <cite>str</cite> or a <code class="xref py py-class docutils literal notranslate"><span class="pre">TermId</span></code> with the query SO term.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a <cite>str</cite> with the concise name for the SO term or <cite>‘n/a’</cite> if a name has not been assigned yet.</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py property">
 <dt class="sig sig-object py" id="gpsea.model.VariantEffect.curie">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">curie</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></em><a class="headerlink" href="#gpsea.model.VariantEffect.curie" title="Link to this definition"></a></dt>
@@ -1649,7 +1687,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="gpsea.data.html" class="btn btn-neutral float-left" title="gpsea.data package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="gpsea.analysis.pscore.stats.html" class="btn btn-neutral float-left" title="gpsea.analysis.pscore.stats package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="gpsea.model.genome.html" class="btn btn-neutral float-right" title="gpsea.model.genome package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
diff --git a/stable/apidocs/gpsea.preprocessing.html b/stable/apidocs/gpsea.preprocessing.html
index aad7a58cd..9e21dc96e 100644
--- a/stable/apidocs/gpsea.preprocessing.html
+++ b/stable/apidocs/gpsea.preprocessing.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.preprocessing package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.preprocessing package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4 current"><a class="current reference internal" href="#">gpsea.preprocessing package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.view.html">gpsea.view package</a></li>
@@ -600,13 +599,8 @@
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.preprocessing.</span></span><span class="sig-name descname"><span class="pre">UniprotProteinMetadataService</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">timeout</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">30.0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/preprocessing/_uniprot.html#UniprotProteinMetadataService"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.preprocessing.UniprotProteinMetadataService" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="#gpsea.preprocessing.ProteinMetadataService" title="gpsea.preprocessing._api.ProteinMetadataService"><code class="xref py py-class docutils literal notranslate"><span class="pre">ProteinMetadataService</span></code></a></p>
 <p>A class that creates ProteinMetadata objects from data found with the Uniprot REST API.
-More info on the Uniprot REST API here - <a class="reference external" href="https://www.uniprot.org/help/programmatic_access">https://www.uniprot.org/help/programmatic_access</a></p>
-<dl class="py method">
-<dt class="sig sig-object py">
-<span class="sig-name descname"><span class="pre">annotate(protein_id</span></span></dt>
-<dd><p>str): Gets metadata and creates ProteinMetadata for given protein ID</p>
-</dd></dl>
-
+More info on the Uniprot REST API are
+in the <a class="reference external" href="https://www.uniprot.org/help/programmatic_access">Programmatic access</a> section.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.preprocessing.UniprotProteinMetadataService.parse_uniprot_json">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">parse_uniprot_json</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">payload</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Mapping" title="(in Python v3.12)"><span class="pre">Mapping</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protein_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="gpsea.model.html#gpsea.model.ProteinMetadata" title="gpsea.model._protein.ProteinMetadata"><span class="pre">ProteinMetadata</span></a></span></span><a class="reference internal" href="../_modules/gpsea/preprocessing/_uniprot.html#UniprotProteinMetadataService.parse_uniprot_json"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.preprocessing.UniprotProteinMetadataService.parse_uniprot_json" title="Link to this definition"></a></dt>
diff --git a/stable/apidocs/gpsea.view.html b/stable/apidocs/gpsea.view.html
index cbcd153f4..20c99379d 100644
--- a/stable/apidocs/gpsea.view.html
+++ b/stable/apidocs/gpsea.view.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gpsea.view package &mdash; GPSEA 0.3.0 documentation</title>
+  <title>gpsea.view package &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -60,7 +60,6 @@
 <li class="toctree-l2 current"><a class="reference internal" href="gpsea.html">gpsea package</a><ul class="current">
 <li class="toctree-l3 current"><a class="reference internal" href="gpsea.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="gpsea.analysis.html">gpsea.analysis package</a></li>
-<li class="toctree-l4"><a class="reference internal" href="gpsea.data.html">gpsea.data package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.model.html">gpsea.model package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="gpsea.preprocessing.html">gpsea.preprocessing package</a></li>
 <li class="toctree-l4 current"><a class="current reference internal" href="#">gpsea.view package</a></li>
@@ -101,6 +100,35 @@
              
   <section id="module-gpsea.view">
 <span id="gpsea-view-package"></span><h1>gpsea.view package<a class="headerlink" href="#module-gpsea.view" title="Link to this heading"></a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="gpsea.view.CohortVariantViewer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.view.</span></span><span class="sig-name descname"><span class="pre">CohortVariantViewer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tx_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/view/_cohort_variant_viewer.html#CohortVariantViewer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.CohortVariantViewer" title="Link to this definition"></a></dt>
+<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p><cite>CohortVariantViewer</cite> creates an HTML report with the cohort variants.</p>
+<p>The report can be either written into an HTML file or displayed in a Jupyter notebook.</p>
+<p>See :ref:show-cohort-variants: for an example usage.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="gpsea.view.CohortVariantViewer.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cohort</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.model.html#gpsea.model.Cohort" title="gpsea.model._cohort.Cohort"><span class="pre">Cohort</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_hgvs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/gpsea/view/_cohort_variant_viewer.html#CohortVariantViewer.process"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.CohortVariantViewer.process" title="Link to this definition"></a></dt>
+<dd><p>Create an HTML that should be shown with <code class="docutils literal notranslate"><span class="pre">display(HTML(..))</span></code> of the ipython package.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cohort</strong> (<a class="reference internal" href="gpsea.model.html#gpsea.model.Cohort" title="gpsea.model.Cohort"><em>Cohort</em></a>) – The cohort being analyzed in the current notebook.</p></li>
+<li><p><strong>only_hgvs</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Do not show the transcript ID part of the HGVS annotation, just the annotation.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>an HTML string with parameterized template for rendering</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.view.CohortViewable">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.view.</span></span><span class="sig-name descname"><span class="pre">CohortViewable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_phenotype_count</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_variant_count</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/view/_cohort.html#CohortViewable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.CohortViewable" title="Link to this definition"></a></dt>
@@ -305,6 +333,21 @@
 
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="gpsea.view.summarize_hpo_analysis">
+<span class="sig-prename descclassname"><span class="pre">gpsea.view.</span></span><span class="sig-name descname"><span class="pre">summarize_hpo_analysis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">result</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.analysis.pcats.html#gpsea.analysis.pcats.HpoTermAnalysisResult" title="gpsea.analysis.pcats._impl.HpoTermAnalysisResult"><span class="pre">HpoTermAnalysisResult</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://pandas.pydata.org/pandas-docs/version/2.0.0/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.0.0)"><span class="pre">DataFrame</span></a></span></span><a class="reference internal" href="../_modules/gpsea/view/_phenotype_analysis.html#summarize_hpo_analysis"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.summarize_hpo_analysis" title="Link to this definition"></a></dt>
+<dd><p>Create a dataframe with counts, frequencies, and p values for the tested HPO terms.</p>
+<p>The HPO terms that were not tested will <em>not</em> be included in the frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>hpo</strong> – HPO data.</p></li>
+<li><p><strong>result</strong> – the HPO term analysis results to show.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.view.VariantTranscriptVisualizer">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.view.</span></span><span class="sig-name descname"><span class="pre">VariantTranscriptVisualizer</span></span><a class="reference internal" href="../_modules/gpsea/view/_txp.html#VariantTranscriptVisualizer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.VariantTranscriptVisualizer" title="Link to this definition"></a></dt>
diff --git a/stable/apidocs/modules.html b/stable/apidocs/modules.html
index e02afc659..32d6540ff 100644
--- a/stable/apidocs/modules.html
+++ b/stable/apidocs/modules.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>API reference &mdash; GPSEA 0.3.0 documentation</title>
+  <title>API reference &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
diff --git a/stable/genindex.html b/stable/genindex.html
index 718edad82..ced2fd0fe 100644
--- a/stable/genindex.html
+++ b/stable/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Index &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
@@ -16,7 +16,7 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=e259d695"></script>
+        <script src="_static/documentation_options.js?v=6c02275b"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -38,7 +38,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -103,7 +103,6 @@ <h1 id="index">Index</h1>
  | <a href="#U"><strong>U</strong></a>
  | <a href="#V"><strong>V</strong></a>
  | <a href="#W"><strong>W</strong></a>
- | <a href="#X"><strong>X</strong></a>
  | <a href="#Y"><strong>Y</strong></a>
  
 </div>
@@ -138,10 +137,10 @@ <h2 id="A">A</h2>
 </li>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.AlleleCounter">AlleleCounter (class in gpsea.analysis.predicate.genotype)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantCoordinates.alt">alt (gpsea.model.VariantCoordinates property)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator.annotate">annotate() (gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator method)</a>
 
       <ul>
@@ -167,20 +166,28 @@ <h2 id="A">A</h2>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.Auditor">Auditor (class in gpsea.preprocessing)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant">autosomal_dominant() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)</a>
+
+      <ul>
+        <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_dominant">(in module gpsea.analysis.predicate.genotype)</a>
 </li>
+      </ul></li>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive">autosomal_recessive() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)</a>
+
+      <ul>
+        <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_recessive">(in module gpsea.analysis.predicate.genotype)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
 <h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantClass.BND">BND (gpsea.model.VariantClass attribute)</a>
+      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.biallelic_predicate">biallelic_predicate() (in module gpsea.analysis.predicate.genotype)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.boolean_predicate">boolean_predicate() (in module gpsea.analysis.predicate.genotype)</a>
+      <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantClass.BND">BND (gpsea.model.VariantClass attribute)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -208,13 +215,19 @@ <h2 id="C">C</h2>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantCoordinates.chrom">chrom (gpsea.model.VariantCoordinates property)</a>
 </li>
-      <li><a href="apidocs/gpsea.model.html#gpsea.model.Genotype.code">code (gpsea.model.Genotype property)</a>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcIssue.code">code (gpsea.analysis.mtc_filter.PhenotypeMtcIssue attribute)</a>
+
+      <ul>
+        <li><a href="apidocs/gpsea.model.html#gpsea.model.Genotype.code">(gpsea.model.Genotype property)</a>
 </li>
+      </ul></li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.CODING_SEQUENCE_VARIANT">CODING_SEQUENCE_VARIANT (gpsea.model.VariantEffect attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Cohort">Cohort (class in gpsea.model)</a>
 </li>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.CohortCreator">CohortCreator (class in gpsea.preprocessing)</a>
+</li>
+      <li><a href="apidocs/gpsea.view.html#gpsea.view.CohortVariantViewer">CohortVariantViewer (class in gpsea.view)</a>
 </li>
       <li><a href="apidocs/gpsea.view.html#gpsea.view.CohortViewable">CohortViewable (class in gpsea.view)</a>
 </li>
@@ -426,8 +439,6 @@ <h2 id="F">F</h2>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.filtering_predicate">filtering_predicate() (in module gpsea.analysis.predicate.genotype)</a>
-</li>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.PhenopacketVariantCoordinateFinder.find_coordinates">find_coordinates() (gpsea.preprocessing.PhenopacketVariantCoordinateFinder method)</a>
 
       <ul>
@@ -449,8 +460,6 @@ <h2 id="F">F</h2>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.FRAMESHIFT_VARIANT">FRAMESHIFT_VARIANT (gpsea.model.VariantEffect attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Genotypes.from_mapping">from_mapping() (gpsea.model.Genotypes static method)</a>
-</li>
-      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.from_moi_info">from_moi_info() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Cohort.from_patients">from_patients() (gpsea.model.Cohort static method)</a>
 </li>
@@ -537,7 +546,7 @@ <h2 id="G">G</h2>
       <ul>
         <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.get_categorizations">(gpsea.analysis.predicate.phenotype.DiseasePresencePredicate method)</a>
 </li>
-        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_categorizations">(gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate method)</a>
+        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.get_categorizations">(gpsea.analysis.predicate.phenotype.HpoPredicate method)</a>
 </li>
         <li><a href="apidocs/gpsea.analysis.predicate.html#gpsea.analysis.predicate.PolyPredicate.get_categorizations">(gpsea.analysis.predicate.PolyPredicate method)</a>
 </li>
@@ -574,23 +583,21 @@ <h2 id="G">G</h2>
         <li><a href="apidocs/gpsea.analysis.pscore.html#gpsea.analysis.pscore.CountingPhenotypeScorer.get_question">(gpsea.analysis.pscore.CountingPhenotypeScorer method)</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.get_question_base">get_question_base() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate method)</a>
 
       <ul>
         <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.get_question_base">(gpsea.analysis.predicate.phenotype.DiseasePresencePredicate method)</a>
 </li>
-        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.get_question_base">(gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate method)</a>
+        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.get_question_base">(gpsea.analysis.predicate.phenotype.HpoPredicate method)</a>
 </li>
         <li><a href="apidocs/gpsea.analysis.predicate.html#gpsea.analysis.predicate.PolyPredicate.get_question_base">(gpsea.analysis.predicate.PolyPredicate method)</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.VVMultiCoordinateService.get_response">get_response() (gpsea.preprocessing.VVMultiCoordinateService method)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.TranscriptCoordinates.get_three_prime_utrs">get_three_prime_utrs() (gpsea.model.TranscriptCoordinates method)</a>
-</li>
-      <li><a href="apidocs/gpsea.data.html#gpsea.data.get_toy_cohort">get_toy_cohort() (in module gpsea.data)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Cohort.get_variant_by_key">get_variant_by_key() (gpsea.model.Cohort method)</a>
 </li>
@@ -669,13 +676,6 @@ <h2 id="G">G</h2>
 
       <ul>
         <li><a href="apidocs/gpsea.config.html#module-gpsea.config">module</a>
-</li>
-      </ul></li>
-      <li>
-    gpsea.data
-
-      <ul>
-        <li><a href="apidocs/gpsea.data.html#module-gpsea.data">module</a>
 </li>
       </ul></li>
       <li>
@@ -750,6 +750,8 @@ <h2 id="H">H</h2>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Genotype.HOMOZYGOUS_REFERENCE">HOMOZYGOUS_REFERENCE (gpsea.model.Genotype attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter">HpoMtcFilter (class in gpsea.analysis.mtc_filter)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate">HpoPredicate (class in gpsea.analysis.predicate.phenotype)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.HpoTermAnalysis">HpoTermAnalysis (class in gpsea.analysis.pcats)</a>
 </li>
@@ -938,8 +940,6 @@ <h2 id="M">M</h2>
         <li><a href="apidocs/gpsea.analysis.pscore.stats.html#module-gpsea.analysis.pscore.stats">gpsea.analysis.pscore.stats</a>
 </li>
         <li><a href="apidocs/gpsea.config.html#module-gpsea.config">gpsea.config</a>
-</li>
-        <li><a href="apidocs/gpsea.data.html#module-gpsea.data">gpsea.data</a>
 </li>
         <li><a href="apidocs/gpsea.io.html#module-gpsea.io">gpsea.io</a>
 </li>
@@ -954,6 +954,8 @@ <h2 id="M">M</h2>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.monoallelic_predicate">monoallelic_predicate() (in module gpsea.analysis.predicate.genotype)</a>
+</li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.FeatureType.MOTIF">MOTIF (gpsea.model.FeatureType attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.ProteinMetadata.motifs">motifs() (gpsea.model.ProteinMetadata method)</a>
@@ -961,6 +963,8 @@ <h2 id="M">M</h2>
       <li><a href="apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_filter_name">mtc_filter_name (gpsea.analysis.pcats.HpoTermAnalysisResult property)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_filter_results">mtc_filter_results (gpsea.analysis.pcats.HpoTermAnalysisResult property)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue">mtc_issue (gpsea.analysis.mtc_filter.PhenotypeMtcResult property)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_name">mtc_name (gpsea.analysis.pcats.HpoTermAnalysisResult property)</a>
 </li>
@@ -992,17 +996,21 @@ <h2 id="N">N</h2>
       </ul></li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.Strand.NEGATIVE">NEGATIVE (gpsea.model.genome.Strand attribute)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.NMD_TRANSCRIPT_VARIANT">NMD_TRANSCRIPT_VARIANT (gpsea.model.VariantEffect attribute)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.analysis.predicate.html#gpsea.analysis.predicate.PatientCategories.NO">NO (gpsea.analysis.predicate.PatientCategories attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Genotype.NO_CALL">NO_CALL (gpsea.model.Genotype attribute)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO">NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.NON_CODING_TRANSCRIPT_EXON_VARIANT">NON_CODING_TRANSCRIPT_EXON_VARIANT (gpsea.model.VariantEffect attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.NON_CODING_TRANSCRIPT_VARIANT">NON_CODING_TRANSCRIPT_VARIANT (gpsea.model.VariantEffect attribute)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.NON_SPECIFIED_TERM">NON_SPECIFIED_TERM (gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.VepFunctionalAnnotator.NONCODING_EFFECTS">NONCODING_EFFECTS (gpsea.preprocessing.VepFunctionalAnnotator attribute)</a>
 </li>
@@ -1020,12 +1028,14 @@ <h2 id="O">O</h2>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Phenotype.observed">observed (gpsea.model.Phenotype property)</a>
 </li>
-      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.ok">ok() (gpsea.analysis.mtc_filter.PhenotypeMtcResult static method)</a>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK">OK (gpsea.analysis.mtc_filter.PhenotypeMtcFilter attribute)</a>
 </li>
-      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.one_genotype_has_zero_hpo_observations">one_genotype_has_zero_hpo_observations() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)</a>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.ok">ok() (gpsea.analysis.mtc_filter.PhenotypeMtcResult static method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.one_genotype_has_zero_hpo_observations">one_genotype_has_zero_hpo_observations() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)</a>
+</li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.Strand.opposite">opposite() (gpsea.model.genome.Strand method)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.TranscriptAnnotation.overlapping_exons">overlapping_exons (gpsea.model.TranscriptAnnotation property)</a>
@@ -1069,11 +1079,11 @@ <h2 id="P">P</h2>
       <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.phenotype">phenotype (gpsea.analysis.predicate.phenotype.DiseasePresencePredicate property)</a>
 
       <ul>
+        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.phenotype">(gpsea.analysis.predicate.phenotype.HpoPredicate property)</a>
+</li>
         <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypeCategorization.phenotype">(gpsea.analysis.predicate.phenotype.PhenotypeCategorization property)</a>
 </li>
         <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.phenotype">(gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate property)</a>
-</li>
-        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.phenotype">(gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate property)</a>
 </li>
       </ul></li>
       <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypeCategorization">PhenotypeCategorization (class in gpsea.analysis.predicate.phenotype)</a>
@@ -1081,17 +1091,15 @@ <h2 id="P">P</h2>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.PhenotypeCreator">PhenotypeCreator (class in gpsea.preprocessing)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcFilter">PhenotypeMtcFilter (class in gpsea.analysis.mtc_filter)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcIssue">PhenotypeMtcIssue (class in gpsea.analysis.mtc_filter)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult">PhenotypeMtcResult (class in gpsea.analysis.mtc_filter)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate">PhenotypePolyPredicate (class in gpsea.analysis.predicate.phenotype)</a>
 </li>
-      <li><a href="apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.phenotypes">phenotypes (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property)</a>
-
-      <ul>
-        <li><a href="apidocs/gpsea.model.html#gpsea.model.Patient.phenotypes">(gpsea.model.Patient property)</a>
+      <li><a href="apidocs/gpsea.model.html#gpsea.model.Patient.phenotypes">phenotypes (gpsea.model.Patient property)</a>
 </li>
-      </ul></li>
       <li><a href="apidocs/gpsea.analysis.pscore.html#gpsea.analysis.pscore.PhenotypeScoreAnalysis">PhenotypeScoreAnalysis (class in gpsea.analysis.pscore)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pscore.html#gpsea.analysis.pscore.PhenotypeScoreAnalysisResult">PhenotypeScoreAnalysisResult (class in gpsea.analysis.pscore)</a>
@@ -1106,6 +1114,16 @@ <h2 id="P">P</h2>
 </li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.Strand.POSITIVE">POSITIVE (gpsea.model.genome.Strand attribute)</a>
 </li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.possible_results">possible_results() (gpsea.analysis.mtc_filter.HpoMtcFilter method)</a>
+
+      <ul>
+        <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcFilter.possible_results">(gpsea.analysis.mtc_filter.PhenotypeMtcFilter method)</a>
+</li>
+        <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.possible_results">(gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter method)</a>
+</li>
+        <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.possible_results">(gpsea.analysis.mtc_filter.UseAllTermsMtcFilter method)</a>
+</li>
+      </ul></li>
       <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.prepare_hpo_terms_of_interest">prepare_hpo_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)</a>
 </li>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.Auditor.prepare_notepad">prepare_notepad() (gpsea.preprocessing.Auditor static method)</a>
@@ -1117,9 +1135,9 @@ <h2 id="P">P</h2>
       <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.present_phenotype_categorization">present_phenotype_categorization (gpsea.analysis.predicate.phenotype.DiseasePresencePredicate property)</a>
 
       <ul>
-        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.present_phenotype_categorization">(gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate property)</a>
+        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.present_phenotype_categorization">(gpsea.analysis.predicate.phenotype.HpoPredicate property)</a>
 </li>
-        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.present_phenotype_categorization">(gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate property)</a>
+        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.present_phenotype_categorization">(gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate property)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -1136,6 +1154,8 @@ <h2 id="P">P</h2>
         <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.PhenopacketPatientCreator.process">(gpsea.preprocessing.PhenopacketPatientCreator method)</a>
 </li>
         <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.PhenotypeCreator.process">(gpsea.preprocessing.PhenotypeCreator method)</a>
+</li>
+        <li><a href="apidocs/gpsea.view.html#gpsea.view.CohortVariantViewer.process">(gpsea.view.CohortVariantViewer method)</a>
 </li>
         <li><a href="apidocs/gpsea.view.html#gpsea.view.CohortViewable.process">(gpsea.view.CohortViewable method)</a>
 </li>
@@ -1147,8 +1167,6 @@ <h2 id="P">P</h2>
 </li>
       </ul></li>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.VepFunctionalAnnotator.process_response">process_response() (gpsea.preprocessing.VepFunctionalAnnotator method)</a>
-</li>
-      <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate">PropagatingPhenotypePredicate (class in gpsea.analysis.predicate.phenotype)</a>
 </li>
       <li><a href="apidocs/gpsea.preprocessing.html#gpsea.preprocessing.ProtCachingMetadataService">ProtCachingMetadataService (class in gpsea.preprocessing)</a>
 </li>
@@ -1212,8 +1230,12 @@ <h2 id="P">P</h2>
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason">reason (gpsea.analysis.mtc_filter.PhenotypeMtcResult property)</a>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcIssue.reason">reason (gpsea.analysis.mtc_filter.PhenotypeMtcIssue attribute)</a>
+
+      <ul>
+        <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason">(gpsea.analysis.mtc_filter.PhenotypeMtcResult property)</a>
 </li>
+      </ul></li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantCoordinates.ref">ref (gpsea.model.VariantCoordinates property)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates.ref_length">ref_length() (gpsea.analysis.predicate.genotype.VariantPredicates static method)</a>
@@ -1226,14 +1248,14 @@ <h2 id="R">R</h2>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.FeatureType.REGION">REGION (gpsea.model.FeatureType attribute)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.TranscriptCoordinates.region">region (gpsea.model.TranscriptCoordinates property)</a>
 
       <ul>
         <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantCoordinates.region">(gpsea.model.VariantCoordinates property)</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates.region">region() (gpsea.analysis.predicate.genotype.VariantPredicates static method)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.ProteinMetadata.regions">regions() (gpsea.model.ProteinMetadata method)</a>
@@ -1254,6 +1276,8 @@ <h2 id="R">R</h2>
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.SAME_COUNT_AS_THE_ONLY_CHILD">SAME_COUNT_AS_THE_ONLY_CHILD (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)</a>
+</li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.SampleLabels">SampleLabels (class in gpsea.model)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pscore.html#gpsea.analysis.pscore.CountingPhenotypeScorer.score">score() (gpsea.analysis.pscore.CountingPhenotypeScorer method)</a>
@@ -1273,6 +1297,14 @@ <h2 id="S">S</h2>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.sex_predicate">sex_predicate() (in module gpsea.analysis.predicate.genotype)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.Genotypes.single">single() (gpsea.model.Genotypes static method)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_GENERAL_TERM">SKIPPING_GENERAL_TERM (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_NON_PHENOTYPE_TERM">SKIPPING_NON_PHENOTYPE_TERM (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SAME_OBSERVED_PROPORTIONS">SKIPPING_SAME_OBSERVED_PROPORTIONS (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS">SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantClass.SNV">SNV (gpsea.model.VariantClass attribute)</a>
 </li>
@@ -1294,6 +1326,8 @@ <h2 id="S">S</h2>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.SPLICE_REGION_VARIANT">SPLICE_REGION_VARIANT (gpsea.model.VariantEffect attribute)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.FeatureInfo.start">start (gpsea.model.FeatureInfo property)</a>
 
       <ul>
@@ -1302,8 +1336,6 @@ <h2 id="S">S</h2>
         <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantCoordinates.start">(gpsea.model.VariantCoordinates property)</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.START_LOST">START_LOST (gpsea.model.VariantEffect attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.GenomicRegion.start_on_strand">start_on_strand() (gpsea.model.genome.GenomicRegion method)</a>
@@ -1331,12 +1363,14 @@ <h2 id="S">S</h2>
 </li>
       </ul></li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.Stranded">Stranded (class in gpsea.model.genome)</a>
+</li>
+      <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.structural_so_id_to_display">structural_so_id_to_display() (gpsea.model.VariantEffect static method)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.ImpreciseSvInfo.structural_type">structural_type (gpsea.model.ImpreciseSvInfo property)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates.structural_type">structural_type() (gpsea.analysis.predicate.genotype.VariantPredicates static method)</a>
 </li>
-      <li><a href="apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.summarize">summarize() (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult method)</a>
+      <li><a href="apidocs/gpsea.view.html#gpsea.view.summarize_hpo_analysis">summarize_hpo_analysis() (in module gpsea.view)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pcats.stats.html#gpsea.analysis.pcats.stats.CountStatistic.supports_shape">supports_shape (gpsea.analysis.pcats.stats.CountStatistic property)</a>
 
@@ -1363,7 +1397,7 @@ <h2 id="T">T</h2>
 </li>
         <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.test">(gpsea.analysis.predicate.phenotype.DiseasePresencePredicate method)</a>
 </li>
-        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate.test">(gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate method)</a>
+        <li><a href="apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate.test">(gpsea.analysis.predicate.phenotype.HpoPredicate method)</a>
 </li>
         <li><a href="apidocs/gpsea.analysis.predicate.html#gpsea.analysis.predicate.PolyPredicate.test">(gpsea.analysis.predicate.PolyPredicate method)</a>
 </li>
@@ -1375,6 +1409,8 @@ <h2 id="T">T</h2>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.TFBS_AMPLIFICATION">TFBS_AMPLIFICATION (gpsea.model.VariantEffect attribute)</a>
 </li>
       <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.THREE_PRIME_UTR_VARIANT">THREE_PRIME_UTR_VARIANT (gpsea.model.VariantEffect attribute)</a>
+</li>
+      <li><a href="apidocs/gpsea.model.html#gpsea.model.VariantEffect.to_display">to_display() (gpsea.model.VariantEffect method)</a>
 </li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.Transposable.to_negative_strand">to_negative_strand() (gpsea.model.genome.Transposable method)</a>
 </li>
@@ -1417,6 +1453,8 @@ <h2 id="T">T</h2>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.Transposable">Transposable (class in gpsea.model.genome)</a>
 </li>
       <li><a href="apidocs/gpsea.model.genome.html#gpsea.model.genome.transpose_coordinate">transpose_coordinate() (in module gpsea.model.genome)</a>
+</li>
+      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates.true">true() (gpsea.analysis.predicate.genotype.VariantPredicates static method)</a>
 </li>
       <li><a href="apidocs/gpsea.analysis.pscore.stats.html#gpsea.analysis.pscore.stats.TTestStatistic">TTestStatistic (class in gpsea.analysis.pscore.stats)</a>
 </li>
@@ -1553,18 +1591,6 @@ <h2 id="W">W</h2>
   </ul></td>
 </tr></table>
 
-<h2 id="X">X</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant">x_dominant() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive">x_recessive() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)</a>
-</li>
-  </ul></td>
-</tr></table>
-
 <h2 id="Y">Y</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
diff --git a/stable/index.html b/stable/index.html
index 4f768aa17..d3a19b77e 100644
--- a/stable/index.html
+++ b/stable/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>GPSEA &mdash; GPSEA 0.3.0 documentation</title>
+  <title>GPSEA &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=e259d695"></script>
+        <script src="_static/documentation_options.js?v=6c02275b"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -42,7 +42,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -92,8 +92,8 @@ <h1>GPSEA<a class="headerlink" href="#gpsea" title="Link to this heading"></a
 A key question in biology and human genetics concerns the relationships between phenotypic abnormalities and genotype. In Mendelian
 genetics, the focus is generally placed on the study of whether specific disease-causing alleles are associated with specific phenotypic
 manifestations of the disease.</p>
-<p><cite>GPSEA</cite>  (genotypes and phenotypes - study and evaluation of associations) is a Python package designed to support genotype-phenotype correlation analysis.
-We pronounce GPSEA as “G”-“P”-“C”. The input to <cite>GPSEA</cite> is a collection of <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/35705716/">Global Alliance for Genomics and Health (GA4GH) Phenopackets</a>.
+<p><cite>GPSEA</cite>  (Genotypes and Phenotypes - Statistical Evaluation of Associations, pronounced “G”-“P”-“C”) is a Python package designed to support genotype-phenotype correlation analysis.
+The input to <cite>GPSEA</cite> is a collection of <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/35705716/">Global Alliance for Genomics and Health (GA4GH) Phenopackets</a>.
 <cite>gpsea</cite> ingests data from these phenopackets and performs analysis of the correlation of specific variants,
 variant types (e.g., missense vs. premature termination codon), or variant location in protein motifs or other features.
 The phenotypic abnormalities are represented by <a class="reference external" href="https://hpo.jax.org/app/">Human Phenotype Ontology (HPO)</a> terms.
diff --git a/stable/installation.html b/stable/installation.html
index ce35e8da6..6c7e55a27 100644
--- a/stable/installation.html
+++ b/stable/installation.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Installation &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Installation &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=e259d695"></script>
+        <script src="_static/documentation_options.js?v=6c02275b"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
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\ No newline at end of file
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\ No newline at end of file
diff --git a/stable/tutorial.html b/stable/tutorial.html
index 3f8b6e838..c6b421711 100644
--- a/stable/tutorial.html
+++ b/stable/tutorial.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Tutorial &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Tutorial &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=e259d695"></script>
+        <script src="_static/documentation_options.js?v=6c02275b"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -58,7 +58,12 @@
 <li class="toctree-l2"><a class="reference internal" href="#the-analysis">The analysis</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#load-hpo">Load HPO</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#prepare-cohort">Prepare cohort</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#explore-cohort">Explore cohort</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#explore-cohort">Explore cohort</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#show-cohort-summary">Show cohort summary</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#plot-distribution-of-variants-with-respect-to-the-protein-sequence">Plot distribution of variants with respect to the protein sequence</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#summarize-all-variant-alleles">Summarize all variant alleles</a></li>
+</ul>
+</li>
 <li class="toctree-l3"><a class="reference internal" href="#prepare-genotype-and-phenotype-predicates">Prepare genotype and phenotype predicates</a></li>
 </ul>
 </li>
@@ -160,7 +165,7 @@ <h3>Prepare cohort<a class="headerlink" href="#prepare-cohort" title="Link to th
 <span class="gp">... </span>    <span class="n">phenopackets</span><span class="o">=</span><span class="n">phenopackets</span><span class="p">,</span>
 <span class="gp">... </span>    <span class="n">cohort_creator</span><span class="o">=</span><span class="n">cohort_creator</span><span class="p">,</span>
 <span class="gp">... </span><span class="p">)</span>
-<span class="go">Patients Created: ...</span>
+<span class="go">Individuals Processed: ...</span>
 </pre></div>
 </div>
 <p>and we will check that there are no Q/C issues:</p>
@@ -178,7 +183,10 @@ <h3>Prepare cohort<a class="headerlink" href="#prepare-cohort" title="Link to th
 </section>
 <section id="explore-cohort">
 <h3>Explore cohort<a class="headerlink" href="#explore-cohort" title="Link to this heading"></a></h3>
-<p>We can now explore the cohort to see how many patients are included.</p>
+<p>GPSEA helps with gaining insight into the cohort by providing</p>
+<section id="show-cohort-summary">
+<h4>Show cohort summary<a class="headerlink" href="#show-cohort-summary" title="Link to this heading"></a></h4>
+<p>The summary report provides an overview about the HPO terms, variants, diseases, and variant effects that occurr most frequently:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.view</span> <span class="kn">import</span> <span class="n">CohortViewable</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">viewer</span> <span class="o">=</span> <span class="n">CohortViewable</span><span class="p">(</span><span class="n">hpo</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">report</span> <span class="o">=</span> <span class="n">viewer</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">cohort</span><span class="o">=</span><span class="n">cohort</span><span class="p">,</span> <span class="n">transcript_id</span><span class="o">=</span><span class="n">tx_id</span><span class="p">)</span>
@@ -528,6 +536,9 @@ <h3>Variant categories for NM_181486.4</h3>
 </pre></div>
 </div>
 </div>
+</section>
+<section id="plot-distribution-of-variants-with-respect-to-the-protein-sequence">
+<h4>Plot distribution of variants with respect to the protein sequence<a class="headerlink" href="#plot-distribution-of-variants-with-respect-to-the-protein-sequence" title="Link to this heading"></a></h4>
 <p>Now we can show the distribution of variants with respect to the encoded protein.
 We first obtain <cite>tx_coordinates</cite> (<a class="reference internal" href="apidocs/gpsea.model.html#gpsea.model.TranscriptCoordinates" title="gpsea.model.TranscriptCoordinates"><code class="xref py py-class docutils literal notranslate"><span class="pre">TranscriptCoordinates</span></code></a>)
 and <cite>protein_meta</cite> (<a class="reference internal" href="apidocs/gpsea.model.html#gpsea.model.ProteinMetadata" title="gpsea.model.ProteinMetadata"><code class="xref py py-class docutils literal notranslate"><span class="pre">ProteinMetadata</span></code></a>)
@@ -557,23 +568,620 @@ <h3>Variant categories for NM_181486.4</h3>
 </div>
 <a class="reference internal image-reference" href="_images/tbx5_protein_diagram.png"><img alt="TBX5 protein diagram" class="align-center" src="_images/tbx5_protein_diagram.png" style="width: 600px;" /></a>
 </section>
+<section id="summarize-all-variant-alleles">
+<span id="show-cohort-variants"></span><h4>Summarize all variant alleles<a class="headerlink" href="#summarize-all-variant-alleles" title="Link to this heading"></a></h4>
+<p>We can prepare a table of all variant alleles that occurr in the cohort.
+Each table row corresponds to a single allele and lists the variant key,
+the predicted effect on the transcript (<em>cDNA</em>) and protein of interest,
+the variant effects, and the number of patients who present
+with one or more variant alleles (<em>Count</em>):</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.view</span> <span class="kn">import</span> <span class="n">CohortVariantViewer</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">viewer</span> <span class="o">=</span> <span class="n">CohortVariantViewer</span><span class="p">(</span><span class="n">tx_id</span><span class="o">=</span><span class="n">tx_id</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">report</span> <span class="o">=</span> <span class="n">viewer</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">cohort</span><span class="o">=</span><span class="n">cohort</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s1">&#39;docs/report/tbx5_all_variants.html&#39;</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>  
+<span class="gp">... </span>    <span class="n">_</span> <span class="o">=</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">report</span><span class="p">)</span>
+</pre></div>
+</div>
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="utf-8">
+  <title>Cohort</title>
+    <style>
+    table {
+      border-collapse: collapse;
+      margin: 25px 0;
+      font-size: 0.9em;
+      font-family: sans-serif;
+      min-width: 400px;
+      box-shadow: 0 0 20px rgba(0, 0, 0, 0.15);
+    }
+
+    .table .column-1 {
+      text-align: left;
+    }
+    th {
+      background-color: LightSkyBlue;
+      border: 1px solid #dddddd;
+      text-align: left;
+      padding: 2px;
+      font-weight: bold;
+      font-size: 120%;
+    }
+
+    tr {
+      border: 1px solid #dddddd;
+    }
+
+    td {
+      padding: 2px;
+      font-weight: bold;
+    }
+
+    tr:nth-child(even) {
+      background-color: #f2f2f2;
+    }
+
+    .table td, tr {
+      text-align: right;
+    }
+
+    .lft {
+      text-align: left;
+    }
+
+    div {
+      display: block;
+      width: 100%;
+      padding-right: 1%;
+      margin-bottom: 20px; /* Add margin to separate divs */
+    }
+
+    caption {
+      caption-side: top;
+      text-align: left;
+      padding-bottom: 10px;
+      font-weight: bold;
+    }
+  </style>
+</head>
+
+<body>
+  <h1>GPSEA cohort analysis: All variant alleles</h1>
+
+
+    <table>
+    <caption style="color: black;">
+        <h3>Variant alleles</h3>
+        A total of 53 unique alleles were identified in the cohort.
+    </caption>
+
+
+        <tbody>
+            <tr class="strng">
+                <th class="lft">Variant key</th>
+                <th>Variant (cDNA)</th>
+                <th>Variant (protein)</th>
+                <th>Effects</th>
+                <th>Count</th>
+            </tr>
+            
+            <tr>
+                <td class="lft">12_114385521_114385521_C_T</td>
+                <td>c.710G>A</td>
+                <td>p.Arg237Gln</td>
+                <td>missense</td>
+                <td>22</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401830_114401830_C_T</td>
+                <td>c.238G>A</td>
+                <td>p.Gly80Arg</td>
+                <td>missense</td>
+                <td>20</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385563_114385563_G_A</td>
+                <td>c.668C>T</td>
+                <td>p.Thr223Met</td>
+                <td>missense</td>
+                <td>8</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398675_114398675_G_T</td>
+                <td>c.408C>A</td>
+                <td>p.Tyr136Ter</td>
+                <td>stop gained</td>
+                <td>6</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399514_114399514_A_C</td>
+                <td>c.361T>G</td>
+                <td>p.Trp121Gly</td>
+                <td>missense, splice region</td>
+                <td>5</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114403792_114403792_C_CG</td>
+                <td>c.106_107insC</td>
+                <td>p.Ser36ThrfsTer25</td>
+                <td>frameshift</td>
+                <td>5</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398682_114398682_C_CG</td>
+                <td>c.400dup</td>
+                <td>p.Arg134ProfsTer49</td>
+                <td>frameshift</td>
+                <td>5</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385474_114385474_A_G</td>
+                <td>c.755+2T>C</td>
+                <td>None</td>
+                <td>splice donor</td>
+                <td>4</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398656_114398656_C_CG</td>
+                <td>c.426dup</td>
+                <td>p.Ala143ArgfsTer40</td>
+                <td>frameshift</td>
+                <td>4</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366360_114366360_C_T</td>
+                <td>c.787G>A</td>
+                <td>p.Val263Met</td>
+                <td>missense</td>
+                <td>4</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385522_114385522_G_A</td>
+                <td>c.709C>T</td>
+                <td>p.Arg237Trp</td>
+                <td>missense</td>
+                <td>4</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114403798_114403798_G_GC</td>
+                <td>c.100dup</td>
+                <td>p.Ala34GlyfsTer27</td>
+                <td>frameshift</td>
+                <td>4</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399613_114399613_T_A</td>
+                <td>c.262A>T</td>
+                <td>p.Lys88Ter</td>
+                <td>stop gained</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401827_114401827_T_A</td>
+                <td>c.241A>T</td>
+                <td>p.Arg81Trp</td>
+                <td>missense, splice region</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366312_114366312_G_A</td>
+                <td>c.835C>T</td>
+                <td>p.Arg279Ter</td>
+                <td>stop gained</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366366_114366366_T_A</td>
+                <td>c.781A>T</td>
+                <td>p.Ser261Cys</td>
+                <td>missense</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114403798_114403799_GC_G</td>
+                <td>c.100del</td>
+                <td>p.Ala34ProfsTer32</td>
+                <td>frameshift</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385475_114385475_C_T</td>
+                <td>c.755+1G>A</td>
+                <td>None</td>
+                <td>splice donor</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401853_114401853_G_T</td>
+                <td>c.215C>A</td>
+                <td>p.Thr72Lys</td>
+                <td>missense</td>
+                <td>3</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385521_114385521_C_G</td>
+                <td>c.710G>C</td>
+                <td>p.Arg237Pro</td>
+                <td>missense</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398568_114398568_C_A</td>
+                <td>c.510+5G>T</td>
+                <td>None</td>
+                <td>splice donor 5th base, intronic</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366207_114366208_GC_G</td>
+                <td>c.939del</td>
+                <td>p.Gln315ArgfsTer79</td>
+                <td>frameshift</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366274_114366274_G_T</td>
+                <td>c.873C>A</td>
+                <td>p.Tyr291Ter</td>
+                <td>stop gained</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366267_114366267_C_A</td>
+                <td>c.880G>T</td>
+                <td>p.Glu294Ter</td>
+                <td>stop gained</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398578_114398579_CA_C</td>
+                <td>c.504del</td>
+                <td>p.Phe168LeufsTer6</td>
+                <td>frameshift</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114394762_114394763_CA_C</td>
+                <td>c.641del</td>
+                <td>p.Val214GlyfsTer12</td>
+                <td>frameshift</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398666_114398667_TG_T</td>
+                <td>c.416del</td>
+                <td>p.Pro139GlnfsTer11</td>
+                <td>frameshift</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114403754_114403754_G_T</td>
+                <td>c.145C>A</td>
+                <td>p.Gln49Lys</td>
+                <td>missense, splice region</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385550_114385550_A_AATTATTCTCAG</td>
+                <td>c.680_681insCTGAGAATAAT</td>
+                <td>p.Ile227_Glu228insTer</td>
+                <td>inframe insertion, stop retainined</td>
+                <td>2</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366348_114366349_CT_C</td>
+                <td>c.798del</td>
+                <td>p.Val267TrpfsTer127</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399559_114399559_T_C</td>
+                <td>c.316A>G</td>
+                <td>p.Ile106Val</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114356064_114356065_TA_T</td>
+                <td>c.1024del</td>
+                <td>p.Tyr342ThrfsTer52</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114355755_114355756_TG_T</td>
+                <td>c.1333del</td>
+                <td>p.His445MetfsTer137</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398632_114398632_G_A</td>
+                <td>c.451C>T</td>
+                <td>p.Gln151Ter</td>
+                <td>stop gained</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401907_114401907_A_G</td>
+                <td>c.161T>C</td>
+                <td>p.Ile54Thr</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114355723_114355723_G_A</td>
+                <td>c.1366C>T</td>
+                <td>p.Gln456Ter</td>
+                <td>stop gained</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398602_114398602_T_G</td>
+                <td>c.481A>C</td>
+                <td>p.Thr161Pro</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398708_114398709_GC_G</td>
+                <td>c.374del</td>
+                <td>p.Gly125AlafsTer25</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114385553_114385553_C_A</td>
+                <td>c.678G>T</td>
+                <td>p.Lys226Asn</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399633_114399633_C_G</td>
+                <td>c.243-1G>C</td>
+                <td>None</td>
+                <td>splice acceptor</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401873_114401874_TA_T</td>
+                <td>c.194del</td>
+                <td>p.Leu65GlnfsTer10</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399594_114399594_A_C</td>
+                <td>c.281T>G</td>
+                <td>p.Leu94Arg</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399622_114399622_G_T</td>
+                <td>c.253C>A</td>
+                <td>p.Pro85Thr</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114394743_114394746_TGTG_T</td>
+                <td>c.658_660del</td>
+                <td>p.His220del</td>
+                <td>inframe deletion</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114394820_114394820_C_G</td>
+                <td>c.584G>C</td>
+                <td>p.Gly195Ala</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401846_114401846_C_G</td>
+                <td>c.222G>C</td>
+                <td>p.Met74Ile</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114366241_114366242_CT_C</td>
+                <td>c.905del</td>
+                <td>p.Gln302ArgfsTer92</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114355784_114355785_CA_C</td>
+                <td>c.1304del</td>
+                <td>p.Leu435ArgfsTer147</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114398626_114398627_CG_C</td>
+                <td>c.456del</td>
+                <td>p.Val153SerfsTer21</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114403859_114403859_G_T</td>
+                <td>c.40C>A</td>
+                <td>p.Pro14Thr</td>
+                <td>missense</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114399625_114399629_ACATC_A</td>
+                <td>c.246_249del</td>
+                <td>p.Met83PhefsTer6</td>
+                <td>frameshift</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114394817_114394817_G_C</td>
+                <td>c.587C>G</td>
+                <td>p.Ser196Ter</td>
+                <td>stop gained</td>
+                <td>1</td>
+                </tr>
+            
+            <tr>
+                <td class="lft">12_114401921_114401921_C_G</td>
+                <td>c.148-1G>C</td>
+                <td>None</td>
+                <td>splice acceptor</td>
+                <td>1</td>
+                </tr>
+            
+                </tbody>
+    </table>
+<!--
+   <table>
+    <caption style="color: black;">
+        <h3>Variant category counts for </h3>
+    </caption>
+        <tbody>
+            <tr class="strng">
+                <th class="lft">Variant effect</th>
+                <th>Annotation Count</th>
+              </tr>
+              
+              <tr>
+                <td class="lft">missense</td>
+                <td>85</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">frameshift</td>
+                <td>38</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">stop gained</td>
+                <td>19</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">splice region</td>
+                <td>10</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">splice donor</td>
+                <td>7</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">splice donor 5th base</td>
+                <td>2</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">intronic</td>
+                <td>2</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">splice acceptor</td>
+                <td>2</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">inframe insertion</td>
+                <td>2</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">stop retainined</td>
+                <td>2</td>
+                </tr>
+            
+              <tr>
+                <td class="lft">inframe deletion</td>
+                <td>1</td>
+                </tr>
+            
+           </tbody>
+    </table>
+ -->
+
+
+</body>
+</html>
+</section>
+</section>
 <section id="prepare-genotype-and-phenotype-predicates">
 <h3>Prepare genotype and phenotype predicates<a class="headerlink" href="#prepare-genotype-and-phenotype-predicates" title="Link to this heading"></a></h3>
 <p>We will create a predicate to bin patients into group
-depending on presence of a missense and frameshift variant to test
+depending on presence of a single allele of a missense or frameshift variant to test
 if there is a difference between frameshift and non-frameshift variants
 in the individuals of the <em>TBX5</em> cohort.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span><span class="p">,</span> <span class="n">groups_predicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">groups_predicate</span><span class="p">(</span>
-<span class="gp">... </span>    <span class="n">predicates</span><span class="o">=</span><span class="p">(</span>
-<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
-<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span>
-<span class="gp">... </span>    <span class="p">),</span>
-<span class="gp">... </span>    <span class="n">group_names</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Missense&#39;</span><span class="p">,</span> <span class="s1">&#39;Frameshift&#39;</span><span class="p">),</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span><span class="p">,</span> <span class="n">monoallelic_predicate</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">monoallelic_predicate</span><span class="p">(</span>
+<span class="gp">... </span>    <span class="n">a_predicate</span><span class="o">=</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
+<span class="gp">... </span>    <span class="n">b_predicate</span><span class="o">=</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
+<span class="gp">... </span>    <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Missense&#39;</span><span class="p">,</span> <span class="s1">&#39;Frameshift&#39;</span><span class="p">)</span>
 <span class="gp">... </span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Genotype group: Missense, Frameshift&#39;</span>
+<span class="go">&#39;Allele group: Missense, Frameshift&#39;</span>
 </pre></div>
 </div>
 <div class="admonition note">
@@ -645,16 +1253,16 @@ <h3>Prepare genotype and phenotype predicates<a class="headerlink" href="#prepar
 <span class="gp">... </span>    <span class="n">pheno_predicates</span><span class="o">=</span><span class="n">pheno_predicates</span><span class="p">,</span>
 <span class="gp">... </span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">result</span><span class="o">.</span><span class="n">total_tests</span>
-<span class="go">17</span>
+<span class="go">16</span>
 </pre></div>
 </div>
-<p>We only tested 1y HPO terms. This is despite the individuals being collectively annotated with
+<p>We only tested 16 HPO terms. This is despite the individuals being collectively annotated with
 260 direct and indirect HPO terms</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span>
 <span class="go">260</span>
 </pre></div>
 </div>
-<p>We can show the reasoning behind <em>not</em> testing 243 (<cite>260 - 17</cite>) HPO terms
+<p>We can show the reasoning behind <em>not</em> testing 244 (<cite>260 - 16</cite>) HPO terms
 by exploring the phenotype MTC filtering report.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.view</span> <span class="kn">import</span> <span class="n">MtcStatsViewer</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">mtc_viewer</span> <span class="o">=</span> <span class="n">MtcStatsViewer</span><span class="p">()</span>
@@ -713,9 +1321,9 @@ <h3>Prepare genotype and phenotype predicates<a class="headerlink" href="#prepar
   <h1>Phenotype testing report</h1>
   <p>Phenotype MTC filter: <em>HPO MTC filter</em></p>
   <p>Multiple testing correction: <em>fdr_bh</em></p>
-  <p>Performed statistical tests for 17 out of the total of 260 HPO terms.</p>
+  <p>Performed statistical tests for 16 out of the total of 260 HPO terms.</p>
     <table>
-      <caption>Using <em>HPO MTC filter</em>, 243 term(s) were omitted from statistical analysis.</caption>
+      <caption>Using <em>HPO MTC filter</em>, 244 term(s) were omitted from statistical analysis.</caption>
         <tbody>
           <tr>
             <th>Code</th>
@@ -724,96 +1332,61 @@ <h1>Phenotype testing report</h1>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
+            <td>HMF01</td>
             <td>Skipping term with maximum frequency that was less than threshold 0.2</td>
             <td>51</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping general term</td>
-            <td>44</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term because all genotypes have same HPO observed proportions</td>
-            <td>41</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 2 observations (not powered for 2x2)</td>
-            <td>26</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 1 observations (not powered for 2x2)</td>
-            <td>24</td>
+            <td>HMF02</td>
+            <td>Skipping term because no genotype has more than one observed HPO count</td>
+            <td>3</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 3 observations (not powered for 2x2)</td>
-            <td>22</td>
+            <td>HMF03</td>
+            <td>Skipping term because of a child term with the same individual counts</td>
+            <td>1</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 4 observations (not powered for 2x2)</td>
-            <td>14</td>
+            <td>HMF04</td>
+            <td>Skipping term because all genotypes have same HPO observed proportions</td>
+            <td>41</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 6 observations (not powered for 2x2)</td>
-            <td>12</td>
+            <td>HMF05</td>
+            <td>Skipping term because one genotype had zero observations</td>
+            <td>2</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 5 observations (not powered for 2x2)</td>
-            <td>4</td>
+            <td>HMF06</td>
+            <td>Skipping term with less than 7 observations (not powered for 2x2)</td>
+            <td>102</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term because no genotype has more than one observed HPO count</td>
-            <td>3</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term because one genotype had zero observations</td>
-            <td>2</td>
+            <td>HMF08</td>
+            <td>Skipping general term</td>
+            <td>44</td>
           </tr>
           
         </tbody>
     </table>
 </body>
 </html>
-<p>and these are the top 20 HPO terms ordered by the p value corrected with the Benjamini-Hochberg procedure:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate</span> <span class="kn">import</span> <span class="n">PatientCategories</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">summarize</span><span class="p">(</span><span class="n">hpo</span><span class="p">,</span> <span class="n">PatientCategories</span><span class="o">.</span><span class="n">YES</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">20</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s1">&#39;docs/report/tbx5_frameshift_vs_missense.csv&#39;</span><span class="p">)</span>  
+<p>and these are the tested HPO terms ordered by the p value corrected with the Benjamini-Hochberg procedure:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.view</span> <span class="kn">import</span> <span class="n">summarize_hpo_analysis</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span> <span class="o">=</span> <span class="n">summarize_hpo_analysis</span><span class="p">(</span><span class="n">hpo</span><span class="p">,</span> <span class="n">result</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s1">&#39;docs/report/tbx5_frameshift_vs_missense.csv&#39;</span><span class="p">)</span>  
 </pre></div>
 </div>
 <table class="docutils align-default" id="id5">
 <caption><span class="caption-text"><em>TBX5</em> frameshift vs missense</span><a class="headerlink" href="#id5" title="Link to this table"></a></caption>
 <thead>
-<tr class="row-odd"><th class="head"><p>Genotype group: Missense, Frameshift</p></th>
+<tr class="row-odd"><th class="head"><p>Allele group</p></th>
 <th class="head"><p>Missense</p></th>
 <th class="head"><p>Missense</p></th>
 <th class="head"><p>Frameshift</p></th>
@@ -836,7 +1409,7 @@ <h1>Phenotype testing report</h1>
 <td><p>52%</p></td>
 <td><p>19/19</p></td>
 <td><p>100%</p></td>
-<td><p>0.0009552459156234353</p></td>
+<td><p>0.0008990549794102921</p></td>
 <td><p>5.6190936213143254e-05</p></td>
 </tr>
 <tr class="row-even"><td><p>Abnormal atrioventricular conduction [HP:0005150]</p></td>
@@ -844,7 +1417,7 @@ <h1>Phenotype testing report</h1>
 <td><p>0%</p></td>
 <td><p>3/3</p></td>
 <td><p>100%</p></td>
-<td><p>0.003695652173913043</p></td>
+<td><p>0.003478260869565217</p></td>
 <td><p>0.00043478260869565214</p></td>
 </tr>
 <tr class="row-odd"><td><p>Atrioventricular block [HP:0001678]</p></td>
@@ -852,82 +1425,74 @@ <h1>Phenotype testing report</h1>
 <td><p>0%</p></td>
 <td><p>2/2</p></td>
 <td><p>100%</p></td>
-<td><p>0.015398550724637682</p></td>
-<td><p>0.0036231884057971015</p></td>
-</tr>
-<tr class="row-even"><td><p>Heart block [HP:0012722]</p></td>
-<td><p>0/22</p></td>
-<td><p>0%</p></td>
-<td><p>2/2</p></td>
-<td><p>100%</p></td>
-<td><p>0.015398550724637682</p></td>
+<td><p>0.01932367149758454</p></td>
 <td><p>0.0036231884057971015</p></td>
 </tr>
-<tr class="row-odd"><td><p>Absent thumb [HP:0009777]</p></td>
+<tr class="row-even"><td><p>Absent thumb [HP:0009777]</p></td>
 <td><p>12/71</p></td>
 <td><p>17%</p></td>
 <td><p>14/31</p></td>
 <td><p>45%</p></td>
-<td><p>0.0191369345329502</p></td>
+<td><p>0.022514040627000236</p></td>
 <td><p>0.005628510156750059</p></td>
 </tr>
-<tr class="row-even"><td><p>Patent ductus arteriosus [HP:0001643]</p></td>
+<tr class="row-odd"><td><p>Patent ductus arteriosus [HP:0001643]</p></td>
 <td><p>3/37</p></td>
 <td><p>8%</p></td>
 <td><p>2/2</p></td>
 <td><p>100%</p></td>
-<td><p>0.038236617183985605</p></td>
+<td><p>0.04318488529014845</p></td>
 <td><p>0.01349527665317139</p></td>
 </tr>
-<tr class="row-odd"><td><p>Triphalangeal thumb [HP:0001199]</p></td>
+<tr class="row-even"><td><p>Triphalangeal thumb [HP:0001199]</p></td>
 <td><p>13/72</p></td>
 <td><p>18%</p></td>
 <td><p>13/32</p></td>
 <td><p>41%</p></td>
-<td><p>0.062175372424826694</p></td>
+<td><p>0.06827099717235872</p></td>
 <td><p>0.02560162393963452</p></td>
 </tr>
-<tr class="row-even"><td><p>Cardiac conduction abnormality [HP:0031546]</p></td>
+<tr class="row-odd"><td><p>Cardiac conduction abnormality [HP:0031546]</p></td>
 <td><p>14/36</p></td>
 <td><p>39%</p></td>
 <td><p>3/3</p></td>
 <td><p>100%</p></td>
-<td><p>0.15811357916621074</p></td>
+<td><p>0.17007174901911745</p></td>
 <td><p>0.07440639019586388</p></td>
 </tr>
-<tr class="row-odd"><td><p>Secundum atrial septal defect [HP:0001684]</p></td>
+<tr class="row-even"><td><p>Secundum atrial septal defect [HP:0001684]</p></td>
 <td><p>14/35</p></td>
 <td><p>40%</p></td>
 <td><p>4/22</p></td>
 <td><p>18%</p></td>
-<td><p>0.2690764879148444</p></td>
+<td><p>0.2849045166157176</p></td>
 <td><p>0.1424522583078588</p></td>
 </tr>
-<tr class="row-even"><td><p>Muscular ventricular septal defect [HP:0011623]</p></td>
+<tr class="row-odd"><td><p>Muscular ventricular septal defect [HP:0011623]</p></td>
 <td><p>6/59</p></td>
 <td><p>10%</p></td>
 <td><p>6/25</p></td>
 <td><p>24%</p></td>
-<td><p>0.2868675985983051</p></td>
+<td><p>0.29999225997208373</p></td>
 <td><p>0.1687456462342971</p></td>
 </tr>
-<tr class="row-odd"><td><p>Pulmonary arterial hypertension [HP:0002092]</p></td>
+<tr class="row-even"><td><p>Pulmonary arterial hypertension [HP:0002092]</p></td>
 <td><p>4/6</p></td>
 <td><p>67%</p></td>
 <td><p>0/2</p></td>
 <td><p>0%</p></td>
-<td><p>0.6623376623376622</p></td>
+<td><p>0.6857142857142857</p></td>
 <td><p>0.42857142857142855</p></td>
 </tr>
-<tr class="row-even"><td><p>Hypoplasia of the ulna [HP:0003022]</p></td>
+<tr class="row-odd"><td><p>Hypoplasia of the ulna [HP:0003022]</p></td>
 <td><p>1/12</p></td>
 <td><p>8%</p></td>
 <td><p>2/10</p></td>
 <td><p>20%</p></td>
-<td><p>0.8095238095238093</p></td>
+<td><p>0.831168831168831</p></td>
 <td><p>0.5714285714285713</p></td>
 </tr>
-<tr class="row-odd"><td><p>Hypoplasia of the radius [HP:0002984]</p></td>
+<tr class="row-even"><td><p>Hypoplasia of the radius [HP:0002984]</p></td>
 <td><p>30/62</p></td>
 <td><p>48%</p></td>
 <td><p>6/14</p></td>
@@ -935,7 +1500,7 @@ <h1>Phenotype testing report</h1>
 <td><p>1.0</p></td>
 <td><p>0.7735491022101784</p></td>
 </tr>
-<tr class="row-even"><td><p>Short thumb [HP:0009778]</p></td>
+<tr class="row-odd"><td><p>Short thumb [HP:0009778]</p></td>
 <td><p>11/41</p></td>
 <td><p>27%</p></td>
 <td><p>8/30</p></td>
@@ -943,6 +1508,14 @@ <h1>Phenotype testing report</h1>
 <td><p>1.0</p></td>
 <td><p>1.0</p></td>
 </tr>
+<tr class="row-even"><td><p>Atrial septal defect [HP:0001631]</p></td>
+<td><p>42/44</p></td>
+<td><p>95%</p></td>
+<td><p>20/20</p></td>
+<td><p>100%</p></td>
+<td><p>1.0</p></td>
+<td><p>1.0</p></td>
+</tr>
 <tr class="row-odd"><td><p>Absent radius [HP:0003974]</p></td>
 <td><p>7/32</p></td>
 <td><p>22%</p></td>
@@ -959,38 +1532,6 @@ <h1>Phenotype testing report</h1>
 <td><p>1.0</p></td>
 <td><p>1.0</p></td>
 </tr>
-<tr class="row-odd"><td><p>Atrial septal defect [HP:0001631]</p></td>
-<td><p>42/44</p></td>
-<td><p>95%</p></td>
-<td><p>20/20</p></td>
-<td><p>100%</p></td>
-<td><p>1.0</p></td>
-<td><p>1.0</p></td>
-</tr>
-<tr class="row-even"><td><p>Abnormal ventricular septum morphology [HP:0010438]</p></td>
-<td><p>31/31</p></td>
-<td><p>100%</p></td>
-<td><p>19/19</p></td>
-<td><p>100%</p></td>
-<td></td>
-<td></td>
-</tr>
-<tr class="row-odd"><td><p>Abnormal cardiac ventricle morphology [HP:0001713]</p></td>
-<td><p>31/31</p></td>
-<td><p>100%</p></td>
-<td><p>19/19</p></td>
-<td><p>100%</p></td>
-<td></td>
-<td></td>
-</tr>
-<tr class="row-even"><td><p>Abnormal heart morphology [HP:0001627]</p></td>
-<td><p>62/62</p></td>
-<td><p>100%</p></td>
-<td><p>30/30</p></td>
-<td><p>100%</p></td>
-<td></td>
-<td></td>
-</tr>
 </tbody>
 </table>
 <p>We see that several HPO terms are significantly associated
@@ -1000,7 +1541,7 @@ <h1>Phenotype testing report</h1>
 but it was observed in 19/19 (100%) patients with a frameshift variant.
 Fisher exact test computed a p value of <cite>~0.0000562</cite>
 and the p value corrected by Benjamini-Hochberg procedure
-is <cite>~0.000955</cite>.</p>
+is <cite>~0.000899</cite>.</p>
 </section>
 </section>
 </section>
diff --git a/stable/user-guide/autosomal_recessive.html b/stable/user-guide/autosomal_recessive.html
index 548f0c083..d3194fe72 100644
--- a/stable/user-guide/autosomal_recessive.html
+++ b/stable/user-guide/autosomal_recessive.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Genotype-Phenotype Correlations in Autosomal Recessive Diseases &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Genotype-Phenotype Correlations in Autosomal Recessive Diseases &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -59,7 +59,6 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="glossary.html">Glossary</a></li>
diff --git a/stable/user-guide/exploratory.html b/stable/user-guide/exploratory.html
index 949d2b9c2..9a741410a 100644
--- a/stable/user-guide/exploratory.html
+++ b/stable/user-guide/exploratory.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Cohort exploratory analysis &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Cohort exploratory analysis &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -59,7 +59,6 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="glossary.html">Glossary</a></li>
diff --git a/stable/user-guide/general_hpo_terms.html b/stable/user-guide/general_hpo_terms.html
index 1fe2e47c3..df296eeec 100644
--- a/stable/user-guide/general_hpo_terms.html
+++ b/stable/user-guide/general_hpo_terms.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>General HPO terms &mdash; GPSEA 0.3.0 documentation</title>
+  <title>General HPO terms &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -39,7 +39,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
diff --git a/stable/user-guide/glossary.html b/stable/user-guide/glossary.html
index c26f1cec0..40d4c7483 100644
--- a/stable/user-guide/glossary.html
+++ b/stable/user-guide/glossary.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Glossary &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Glossary &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -61,7 +61,6 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Glossary</a><ul>
diff --git a/stable/user-guide/index.html b/stable/user-guide/index.html
index 194f18f17..73382ef4d 100644
--- a/stable/user-guide/index.html
+++ b/stable/user-guide/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>User guide &mdash; GPSEA 0.3.0 documentation</title>
+  <title>User guide &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -61,7 +61,6 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="glossary.html">Glossary</a></li>
@@ -97,14 +96,16 @@
              
   <section id="user-guide">
 <span id="rstuser-guide"></span><h1>User guide<a class="headerlink" href="#user-guide" title="Link to this heading"></a></h1>
-<p>TODO - write high level overview and bridge to individual sections.</p>
+<p>GPSEA allows users to perform many different kinds of genotype-phenotype correlation (GPCs) analysis. See the <a class="reference internal" href="../tutorial.html#tutorial"><span class="std std-ref">Tutorial</span></a> for an introduction.
+In general, the analysis will include steps for data input, exploration of the cohort to assist in generating hypotheses about potential GPCs to test,
+corresponding choice of genotype and phenotype predicates to perform the test, choice of statistical test, and approach to multiple-testing correction (mtc).
+The pages shown in the table of contents provide more information about each step.</p>
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l1"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l1"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l1"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l1"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="glossary.html">Glossary</a></li>
diff --git a/stable/user-guide/input-data.html b/stable/user-guide/input-data.html
index 2e2163777..514c97c16 100644
--- a/stable/user-guide/input-data.html
+++ b/stable/user-guide/input-data.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Input data &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Input data &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -41,7 +41,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -67,7 +67,6 @@
 </li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="glossary.html">Glossary</a></li>
@@ -168,7 +167,7 @@ <h3>Load phenopackets<a class="headerlink" href="#load-phenopackets" title="Link
 loader function:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">load_phenopackets</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">cohort</span><span class="p">,</span> <span class="n">qc_results</span> <span class="o">=</span> <span class="n">load_phenopackets</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">cohort_creator</span><span class="p">)</span>  
-<span class="go">Patients Created: ...</span>
+<span class="go">Individuals Processed: ...</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">cohort</span><span class="p">)</span>
 <span class="go">19</span>
 </pre></div>
diff --git a/stable/user-guide/mtc.html b/stable/user-guide/mtc.html
index f52462583..0b184cf36 100644
--- a/stable/user-guide/mtc.html
+++ b/stable/user-guide/mtc.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Multiple-testing correction &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Multiple-testing correction &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -61,7 +61,6 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Multiple-testing correction</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#background">Background</a></li>
@@ -278,28 +277,29 @@ <h3>Multiple-testing correction procedures<a class="headerlink" href="#multiple-
 for creating <a class="reference internal" href="../apidocs/gpsea.analysis.mtc_filter.html#gpsea.analysis.mtc_filter.HpoMtcFilter" title="gpsea.analysis.mtc_filter.HpoMtcFilter"><code class="xref py py-class docutils literal notranslate"><span class="pre">HpoMtcFilter</span></code></a>.
 The constructor takes a threshold as an argument (e.g. 20% in the example above)
 and the method’s logic is made up of 8 individual heuristics
-designed to skip testing the HPO terms that are unlikely to yield significant or interesting results:</p>
-<ol class="arabic">
-<li><dl>
-<dt>Skip terms that occur very rarely</dt><dd><p>The <code class="docutils literal notranslate"><span class="pre">term_frequency_threshold</span></code> determines the mininum proportion of individuals
+designed to skip testing the HPO terms that are unlikely to yield significant or interesting results.</p>
+<section id="hmf01-skip-terms-that-occur-very-rarely">
+<h5><cite>HMF01</cite> - Skip terms that occur very rarely<a class="headerlink" href="#hmf01-skip-terms-that-occur-very-rarely" title="Link to this heading"></a></h5>
+<p>The <code class="docutils literal notranslate"><span class="pre">term_frequency_threshold</span></code> determines the mininum proportion of individuals
 with direct or indirect annotation by the HPO term to test.
-We check each of the genotype groups (e.g., MISSENSE vs. not-MISSENSE), and we only retain a term for testing
-if the proportion of individuals in at least one genotype group is greater than or equal to <code class="docutils literal notranslate"><span class="pre">term_frequency_threshold</span></code>.</p>
-<p>This is because of our assumption that even if there is statistical significance,
-if a term is only seen in (for example) 7% of individuals in the MISSENSE group and 2% in the not-MISSENSE group,
+We check each of the genotype groups (e.g., MISSENSE vs. not-MISSENSE),
+and we only retain a term for testing if the proportion of individuals
+in at least one genotype group is greater than
+or equal to <code class="docutils literal notranslate"><span class="pre">term_frequency_threshold</span></code>.
+This is because of our assumption that even if there is statistical significance,
+if a term is only seen in (for example) 7% of individuals
+in the MISSENSE group and 2% in the not-MISSENSE group,
 the term is unlikely to be of great interest because it is rare.</p>
-</dd>
-</dl>
-</li>
-<li><dl class="simple">
-<dt>Skip terms if no cell has more than one count</dt><dd><p>In a related heuristic, we skip terms if no genotype group has more than one count.
-This is not completely redundant with the previous condition,
+</section>
+<section id="hmf02-skip-terms-if-no-genotype-group-has-more-than-one-count">
+<h5><cite>HMF02</cite> - Skip terms if no genotype group has more than one count<a class="headerlink" href="#hmf02-skip-terms-if-no-genotype-group-has-more-than-one-count" title="Link to this heading"></a></h5>
+<p>In a related heuristic, we skip terms if no genotype group has more
+than one count. This is not completely redundant with the previous condition,
 because some terms may have a small number of total observations.</p>
-</dd>
-</dl>
-</li>
-<li><dl>
-<dt>Skip terms if all counts are identical to counts for a child term</dt><dd><p>Let’s say a term such as
+</section>
+<section id="hmf03-skip-terms-if-all-counts-are-identical-to-counts-for-a-child-term">
+<h5><cite>HMF03</cite> - Skip terms if all counts are identical to counts for a child term<a class="headerlink" href="#hmf03-skip-terms-if-all-counts-are-identical-to-counts-for-a-child-term" title="Link to this heading"></a></h5>
+<p>Let’s say a term such as
 <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0001115">Posterior polar cataract (HP:0001115)</a>
 was observed in 7 of 11 individuals with MISSENSE variants
 and in 3 of 8 individuals with NONSENSE variants.
@@ -308,46 +308,49 @@ <h3>Multiple-testing correction procedures<a class="headerlink" href="#multiple-
 then we choose to not test the parent term.</p>
 <p>This is because the more specific an HPO term is,
 the more information it has (the more interesting the correlation would be if it exists),
-and the result of the Fisher Exact test for <em>Polar cataract</em>
-would be exactly the same as for <em>Posterior polar cataract</em>.</p>
-</dd>
-</dl>
-</li>
-<li><dl class="simple">
-<dt>Skip terms if genotypes have same HPO proportions</dt><dd><p>If both (or all) of the genotype groups have the same proportion of individuals
+and the result of a test, such as the Fisher Exact test, would be exactly the same
+for <em>Polar cataract</em> as for <em>Posterior polar cataract</em>.</p>
+</section>
+<section id="hmf04-skip-terms-if-genotypes-have-same-hpo-proportions">
+<h5><cite>HMF04</cite> - Skip terms if genotypes have same HPO proportions<a class="headerlink" href="#hmf04-skip-terms-if-genotypes-have-same-hpo-proportions" title="Link to this heading"></a></h5>
+<p>If both (or all) of the genotype groups have the same proportion of individuals
 observed to be annotated to an HPO term, e.g., both are 50%, then skip the term,
 because it is not possible that the Fisher exact test will return a significant result.</p>
-</dd>
-</dl>
-</li>
-<li><dl class="simple">
-<dt>Skip terms if there are no HPO observations in a group</dt><dd><p>If one of the genotype groups has neither observed nor excluded observations for an HPO term, skip it.</p>
-</dd>
-</dl>
-</li>
-<li><dl class="simple">
-<dt>Skipping terms that are not descendents of <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000118">Phenotypic abnormality (HP:0000118)</a></dt><dd><p>The HPO has a number of other branches that describe modes of inheritance,
+</section>
+<section id="hmf05-skip-term-if-one-of-the-genotype-groups-has-neither-observed-nor-excluded-observations">
+<h5><cite>HMF05</cite> - Skip term if one of the genotype groups has neither observed nor excluded observations<a class="headerlink" href="#hmf05-skip-term-if-one-of-the-genotype-groups-has-neither-observed-nor-excluded-observations" title="Link to this heading"></a></h5>
+<p>Skip terms if there are no HPO observations in a group.</p>
+</section>
+<section id="hmf06-skip-term-if-underpowered-for-2x2-or-2x3-analysis">
+<h5><cite>HMF06</cite> - Skip term if underpowered for 2x2 or 2x3 analysis<a class="headerlink" href="#hmf06-skip-term-if-underpowered-for-2x2-or-2x3-analysis" title="Link to this heading"></a></h5>
+<p>If the individuals are binned into 2 phenotype groups and 2 genotype groups (2x2)
+and the total count of patients in all genotype-phenotype groups is less than 7,
+or into 2 phenotype groups and 3 genotype groups (2x3) and the total count of patients
+is less than 6, then there is a lack even of the nominal statistical power
+and the counts can never be significant.</p>
+</section>
+<section id="hmf07-skipping-terms-that-are-not-descendents-of-phenotypic-abnormality">
+<h5><cite>HMF07</cite> - Skipping terms that are not descendents of <em>Phenotypic abnormality</em><a class="headerlink" href="#hmf07-skipping-terms-that-are-not-descendents-of-phenotypic-abnormality" title="Link to this heading"></a></h5>
+<p>The HPO has a number of other branches that describe modes of inheritance,
 past medical history, and clinical modifiers.
 We do not think it makes much sense to test for enrichment of these terms,
-and so they are filtered out.</p>
-</dd>
-</dl>
-</li>
-<li><dl>
-<dt>Skipping “general” level terms</dt><dd><p>All the direct children of the root phenotype term
-<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000118">Phenotypic abnormality (HP:0000118)</a> are skipped,
-because of the assumption that if there is a valid signal,
+so, all terms that are not descendants of
+<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000118">Phenotypic abnormality</a> are filtered out.</p>
+</section>
+<section id="hmf08-skipping-general-level-terms">
+<h5><cite>HMF08</cite> - Skipping “general” level terms<a class="headerlink" href="#hmf08-skipping-general-level-terms" title="Link to this heading"></a></h5>
+<p>All the direct children of the root phenotype term
+<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000118">Phenotypic abnormality (HP:0000118)</a>
+are skipped, because of the assumption that if there is a valid signal,
 it will derive from one of the more specific descendents.</p>
-<p>For instance, <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000707">Abnormality of the nervous system (HP:0000707)</a>
-is a child of <em>Phenotypic abnormality</em>, and this assumption implies
+<p>For instance,
+<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000707">Abnormality of the nervous system</a>
+(HP:0000707) is a child of <em>Phenotypic abnormality</em>, and this assumption implies
 that if there is a signal from the nervous system,
 it will lead to at least one of the descendents of
 <em>Abnormality of the nervous system</em> being significant.</p>
 <p>See <a class="reference internal" href="general_hpo_terms.html#general-hpo-terms"><span class="std std-ref">General HPO terms</span></a> section for details.</p>
-</dd>
-</dl>
-</li>
-</ol>
+</section>
 </section>
 </section>
 </section>
diff --git a/stable/user-guide/phenotype_predicates.html b/stable/user-guide/phenotype_predicates.html
deleted file mode 100644
index 8efbf9fe6..000000000
--- a/stable/user-guide/phenotype_predicates.html
+++ /dev/null
@@ -1,143 +0,0 @@
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-      <li class="breadcrumb-item active">Phenotype Predicates</li>
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-           <div itemprop="articleBody">
-             
-  <section id="phenotype-predicates">
-<span id="id1"></span><h1>Phenotype Predicates<a class="headerlink" href="#phenotype-predicates" title="Link to this heading"></a></h1>
-<p>GPSEA offers several phenotype predicates.</p>
-<p>TODO – separate explanations for HPO (Fisher), scores (Mann Whitney) and survival (log rank test).</p>
-<div class="toctree-wrapper compound">
-<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="devries.html">De Vries Score</a></li>
-</ul>
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-</section>
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diff --git a/stable/user-guide/predicates.html b/stable/user-guide/predicates.html
index c202ded3d..759b02d17 100644
--- a/stable/user-guide/predicates.html
+++ b/stable/user-guide/predicates.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Predicates &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Predicates &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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@@ -17,7 +17,7 @@
   
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         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Phenotype Predicates" href="phenotype_predicates.html" />
+    <link rel="next" title="Phenotype Predicates" href="predicates/phenotype_predicates.html" />
     <link rel="prev" title="Cohort exploratory analysis" href="exploratory.html" /> 
 </head>
 
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -61,25 +61,12 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Predicates</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#genotype-predicates">Genotype predicates</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#variant-predicates">Variant predicates</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#mode-of-inheritance-predicate">Mode of inheritance predicate</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#filtering-predicate">Filtering predicate</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#groups-predicate">Groups predicate</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#partition-by-the-sex-of-the-individual">Partition by the sex of the individual</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#partition-by-a-diagnosis">Partition by a diagnosis</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#phenotype-predicates">Phenotype predicates</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#propagating-phenotype-predicate">Propagating phenotype predicate</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#predicates-for-all-cohort-phenotypes">Predicates for all cohort phenotypes</a></li>
-</ul>
-</li>
+<li class="toctree-l3"><a class="reference internal" href="predicates/phenotype_predicates.html">Phenotype Predicates</a></li>
+<li class="toctree-l3"><a class="reference internal" href="predicates/genotype_predicates.html">Genotype Predicates</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gallery">Gallery</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#need-more">Need more?</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mtc.html">Multiple-testing correction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="glossary.html">Glossary</a></li>
@@ -116,490 +103,29 @@
              
   <section id="predicates">
 <span id="id1"></span><h1>Predicates<a class="headerlink" href="#predicates" title="Link to this heading"></a></h1>
-<p>Searching for genotype-phenotype associations usually requires to partition
-the individuals into several discrete groups to allow testing for the inter-group differences.
-GPSEA reflects these requirements with its predicate API.
-Perhaps unsurprisingly, a predicate must be capable of partitioning the individuals into two or more groups.
+<p>Searching for genotype-phenotype associations usually requires that
+the individuals are partitioned into two or more discrete groups to allow testing for the inter-group differences.
+GPSEA reflects these requirements with its predicate API.</p>
+<p>A <strong>predicate</strong> must be capable of partitioning the individuals into two or more groups.
 The groups must be <em>exclusive</em> - each individual must be assigned at most into one group.
-Moreover, the groups should be <em>exhaustive</em> and cover maximum of the possible states.
+In general, it is desirable that the groups cover all or at least the majority of the cohort being analyzed to maximize statistical power.
 However, the predicate is allowed to return <cite>None</cite> if the individual cannot be assigned.
-In result, the individual will be omitted from the downstream analysis.</p>
-<p>Predicates serve both <em>genotype</em> and <em>phenotype</em> prongs of the analysis.
+As a result, the individual will be omitted from the downstream analysis.</p>
+<p>Predicates serve both the <em>genotype</em> and <em>phenotype</em> prongs of the analysis.
 Genotype predicates (<a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype.GenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a>)
 assign the <a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Patient" title="gpsea.model.Patient"><code class="xref py py-class docutils literal notranslate"><span class="pre">Patient</span></code></a>
 into a group (mostly) based on the variant information, while the
 phenotype predicates (<a class="reference internal" href="../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate" title="gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhenotypePolyPredicate</span></code></a>)
 use the HPO terms to assign a group.</p>
-<p>It is literally impossible to use GPSEA without the predicates
-because all analyses need at least one predicate (typically a <em>genotype</em> predicate).
-Luckily, the purpose of this guide is to show all that is to know about predicates.
-We will first discuss the genotype predicates and end with phenotype predicates.</p>
-<section id="genotype-predicates">
-<span id="id2"></span><h2>Genotype predicates<a class="headerlink" href="#genotype-predicates" title="Link to this heading"></a></h2>
-<p>A genotype predicate seeks to divide the individuals along an axis that is orthogonal to phenotypes.
-Typically, this includes using the genotype data, such as presence of a missense variant
-in a heterozygous genotype. However, other categorical variables,
-such as diagnoses (TODO - add link to disease predicate) or cluster ids can also be used.</p>
-<p>The genotype predicates test the individual for a presence of variants that meet certain inclusion criteria.
-The testing is done in two steps. First, we count the alleles
-of the matching variants and then we interpret the count, possibly including factors
-such as the expected mode of inheritance and sex, to assign the individual into a group.
-Finding the matching variants is what
-the <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> is all about.</p>
-<p>TODO: wordsmith
-We must first create the variant predicate and then wrap it in genotype predicate.</p>
-<section id="variant-predicates">
-<h3>Variant predicates<a class="headerlink" href="#variant-predicates" title="Link to this heading"></a></h3>
-<p>GPSEA uses the <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> class
-to test if a <a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Variant" title="gpsea.model.Variant"><code class="xref py py-class docutils literal notranslate"><span class="pre">Variant</span></code></a> meets the inclusion criteria.
-The variant predicate can leverage multiple primary data:</p>
-<table class="docutils align-default">
-<thead>
-<tr class="row-odd"><th class="head"><p>Primary data source</p></th>
-<th class="head"><p>Example</p></th>
-</tr>
-</thead>
-<tbody>
-<tr class="row-even"><td><p>Allele</p></td>
-<td><p>the variant being a deletion or a single nucleotide variant (SNV)</p></td>
-</tr>
-<tr class="row-odd"><td><p>Genome</p></td>
-<td><p>overlaps of a target genomic region</p></td>
-</tr>
-<tr class="row-even"><td><p>Functional annotation</p></td>
-<td><p>variant is predicted to lead to a missense change or affect an exon of certain transcript</p></td>
-</tr>
-<tr class="row-odd"><td><p>Protein data</p></td>
-<td><p>variant is located in a region encoding a protein domain, protein feature type</p></td>
-</tr>
-</tbody>
-</table>
-<p>which demands a considerable amount of flexibility for creating the predicate.</p>
-<p>As a rule of thumb, the predicates for testing basic conditions are available off the shelf,
-and they can be used as building block for testing for more complex conditions,
-such as testing if the variant is “a missense or synonymous variant located in exon 6 of transcript <cite>NM_013275.6</cite>”.</p>
-<p>Let’s demonstrate this on few examples.
-We will load a cohort of 19 subjects with variants in <em>RERE</em>,
-leading to <a class="reference external" href="https://omim.org/entry/142900">Holt-Oram syndrome MIM:142900</a>.
-The the clinical signs and symptoms of the subjects were encoded into HPO terms
-along with the pathogenic <em>RERE</em> variant.</p>
-<p>Let’s load the phenopackets, as previously described in greater detail the <a class="reference internal" href="input-data.html#input-data"><span class="std std-ref">Input data</span></a> section.
-Briefly, we first load HPO:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">hpotk</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">store</span> <span class="o">=</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">configure_ontology_store</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">hpo</span> <span class="o">=</span> <span class="n">store</span><span class="o">.</span><span class="n">load_minimal_hpo</span><span class="p">(</span><span class="n">release</span><span class="o">=</span><span class="s1">&#39;v2024-07-01&#39;</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>then, we configure the cohort creator:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">configure_caching_cohort_creator</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">cohort_creator</span> <span class="o">=</span> <span class="n">configure_caching_cohort_creator</span><span class="p">(</span><span class="n">hpo</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>which we use to create a <a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Cohort" title="gpsea.model.Cohort"><code class="xref py py-class docutils literal notranslate"><span class="pre">Cohort</span></code></a> from a bunch of phenopackets
-from the release <cite>0.1.18</cite> of <a class="reference external" href="https://github.com/monarch-initiative/phenopacket-store">Phenopacket Store</a>.
-We will load 19 individuals with mutations in <em>RERE</em> gene:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">ppktstore.registry</span> <span class="kn">import</span> <span class="n">configure_phenopacket_registry</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">registry</span> <span class="o">=</span> <span class="n">configure_phenopacket_registry</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="k">with</span> <span class="n">registry</span><span class="o">.</span><span class="n">open_phenopacket_store</span><span class="p">(</span><span class="n">release</span><span class="o">=</span><span class="s1">&#39;0.1.18&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">ps</span><span class="p">:</span>
-<span class="gp">... </span>    <span class="n">phenopackets</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">iter_cohort_phenopackets</span><span class="p">(</span><span class="s1">&#39;RERE&#39;</span><span class="p">))</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">)</span>
-<span class="go">19</span>
-</pre></div>
-</div>
-<p>and we will convert the phenopacket into a <a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Cohort" title="gpsea.model.Cohort"><code class="xref py py-class docutils literal notranslate"><span class="pre">Cohort</span></code></a>:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">load_phenopackets</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">cohort</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">load_phenopackets</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">cohort_creator</span><span class="p">)</span>  
-<span class="go">Patients Created: ...</span>
-</pre></div>
-</div>
-<p>To demonstrate the predicate API, we will use the variant <code class="docutils literal notranslate"><span class="pre">1_8358231_8358231_T_C</span></code> that corresponds
-to a pathogenic variant <a class="reference external" href="https://www.ncbi.nlm.nih.gov/clinvar/variation/522858/">VCV000522858.5</a>
-that replaces the histidine encoded by the 1435th codon of <cite>NM_001042681.2</cite> with arginine: <code class="docutils literal notranslate"><span class="pre">NM_001042681.2(RERE):c.4304A&gt;G</span> <span class="pre">(p.His1435Arg)</span></code>.</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">variant_key_of_interest</span> <span class="o">=</span> <span class="s1">&#39;1_8358231_8358231_T_C&#39;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">variant</span> <span class="o">=</span> <span class="n">cohort</span><span class="o">.</span><span class="n">get_variant_by_key</span><span class="p">(</span><span class="n">variant_key_of_interest</span><span class="p">)</span>
-</pre></div>
-</div>
-<section id="building-blocks">
-<h4>Building blocks<a class="headerlink" href="#building-blocks" title="Link to this heading"></a></h4>
-<p>We can check that the variant overlaps with <em>RERE</em>:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gene</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">gene</span><span class="p">(</span><span class="s1">&#39;RERE&#39;</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gene</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
-<span class="go">True</span>
-</pre></div>
-</div>
-<p>it overlaps with the <em>MANE</em> transcript:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">rere_mane_tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_001042681.2&#39;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tx</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">transcript</span><span class="p">(</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tx</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
-<span class="go">True</span>
-</pre></div>
-</div>
-<p>it in fact overlaps with the exon 20:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">exon20</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">exon</span><span class="p">(</span><span class="n">exon</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">exon20</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
-<span class="go">True</span>
-</pre></div>
-</div>
-<p>and leads to a missense mutation with respect to the MANE transcript:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">missense</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">missense</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
-<span class="go">True</span>
-</pre></div>
-</div>
-<p>See <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates" title="gpsea.analysis.predicate.genotype.VariantPredicates"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicates</span></code></a>
-for more info on the predicates available off the shelf.</p>
-</section>
-<section id="complex-conditions">
-<h4>Complex conditions<a class="headerlink" href="#complex-conditions" title="Link to this heading"></a></h4>
-<p>We can combine the building blocks to test for more elaborate conditions.
-For instance, we can test if the variant meets <em>any</em> or several conditions:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">nonsense</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_GAINED</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">missense_or_nonsense</span> <span class="o">=</span> <span class="n">missense</span> <span class="o">|</span> <span class="n">nonsense</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">missense_or_nonsense</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
-<span class="go">True</span>
-</pre></div>
-</div>
-<p>or <em>all</em> conditions:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">missense_and_exon20</span> <span class="o">=</span> <span class="n">missense</span> <span class="o">&amp;</span> <span class="n">exon20</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">missense_and_exon20</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
-<span class="go">True</span>
-</pre></div>
-</div>
-<p>The <cite>VariantPredicate</cite> overloads Python <code class="docutils literal notranslate"><span class="pre">&amp;</span></code> (AND) and <code class="docutils literal notranslate"><span class="pre">|</span></code> (OR) operators to build a compound predicate from lower level building blocks.</p>
-<p>Therefore, there is nothing that prevents us to combine the predicates into multi-level tests,
-such as testing if the variant is a <em>“chromosomal deletion” or a deletion which removes at least 50 bp</em>:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantClass</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">chromosomal_deletion</span> <span class="o">=</span> <span class="s2">&quot;SO:1000029&quot;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">predicate</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">structural_type</span><span class="p">(</span><span class="n">chromosomal_deletion</span><span class="p">)</span> <span class="o">|</span> <span class="p">(</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_class</span><span class="p">(</span><span class="n">VariantClass</span><span class="o">.</span><span class="n">DEL</span><span class="p">)</span> <span class="o">&amp;</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">change_length</span><span class="p">(</span><span class="s2">&quot;&lt;=&quot;</span><span class="p">,</span> <span class="o">-</span><span class="mi">50</span><span class="p">))</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">predicate</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
-<span class="go">&#39;(structural type is SO:1000029 OR (variant class is DEL AND change length &lt;= -50))&#39;</span>
-</pre></div>
-</div>
-</section>
-<section id="inverting-conditions">
-<h4>Inverting conditions<a class="headerlink" href="#inverting-conditions" title="Link to this heading"></a></h4>
-<p>Sometimes we may want to test the variant for a condition that must <em>not</em> be met.
-For instance, we may want to test if the variant is a deletion
-that is <em>not</em> predicted to shift the transcript reading frame.
-One of doing this would be to build a compound predicates
-for all variant effects except of <a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.VariantEffect.FRAMESHIFT_VARIANT" title="gpsea.model.VariantEffect.FRAMESHIFT_VARIANT"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRAMESHIFT_VARIANT</span></code></a>:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_effects</span> <span class="o">=</span> <span class="p">(</span>
-<span class="gp">... </span>  <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SYNONYMOUS_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INTRON_VARIANT</span><span class="p">,</span>
-<span class="gp">... </span>  <span class="c1"># and many more effects..</span>
-<span class="gp">... </span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_predicate</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">eff</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span> <span class="k">for</span> <span class="n">eff</span> <span class="ow">in</span> <span class="n">non_frameshift_effects</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>However, this is clearly tedious and it would be much better implemented
-by a simple logical not of a predicate for a frameshift variant effect.</p>
-<p>To support this, <cite>VariantPredicate</cite> implements <em>logical inversion</em>
-which corresponds to Python’s <code class="docutils literal notranslate"><span class="pre">~</span></code> operator (tilde), to wrap
-the underlying predicate and to invert its test result.</p>
-<p>This is how we can use the predicate inversion to build the predicate for non-frameshift deletions:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_del</span> <span class="o">=</span> <span class="o">~</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span> <span class="o">&amp;</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_class</span><span class="p">(</span><span class="n">VariantClass</span><span class="o">.</span><span class="n">DEL</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_del</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
-<span class="go">&#39;(NOT FRAMESHIFT_VARIANT on NM_001042681.2 AND variant class is DEL)&#39;</span>
-</pre></div>
-</div>
-<p>Note the presence of a tilde <code class="docutils literal notranslate"><span class="pre">~</span></code> before the variant effect predicate and resulting <code class="docutils literal notranslate"><span class="pre">NOT</span></code> in the predicate question.</p>
-<p>The variant predicate offers a flexible API for testing if variants meet a condition.
-However, the genotype phenotype correlations are done on the individual level
-and the variant predicates are used as a component of the genotype predicate.
-The next sections show how to use variant predicates to assign individuals into groups.</p>
-</section>
-</section>
-<section id="mode-of-inheritance-predicate">
-<h3>Mode of inheritance predicate<a class="headerlink" href="#mode-of-inheritance-predicate" title="Link to this heading"></a></h3>
-<p>The <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModeOfInheritancePredicate</span></code></a>
-assigns the individual into a group based on the number of alleles
-that match a condition specified by a <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a>.
-The <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModeOfInheritancePredicate</span></code></a> supports
-the following Mendelian modes of inheritance (MoI):</p>
-<table class="docutils align-default">
-<thead>
-<tr class="row-odd"><th class="head"><p>Mode of inheritance</p></th>
-<th class="head"><p>Sex</p></th>
-<th class="head"><p>Allele count</p></th>
-<th class="head"><p>Genotype category</p></th>
-</tr>
-</thead>
-<tbody>
-<tr class="row-even"><td rowspan="3"><p>Autosomal dominant</p></td>
-<td><p><cite>*</cite></p></td>
-<td><p>0</p></td>
-<td><p><cite>HOM_REF</cite></p></td>
-</tr>
-<tr class="row-odd"><td><p><cite>*</cite></p></td>
-<td><p>1</p></td>
-<td><p><cite>HET</cite></p></td>
-</tr>
-<tr class="row-even"><td><p><cite>*</cite></p></td>
-<td><p><span class="math notranslate nohighlight">\(\ge 2\)</span></p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
-</tr>
-<tr class="row-odd"><td rowspan="4"><p>Autosomal recessive</p></td>
-<td><p><cite>*</cite></p></td>
-<td><p>0</p></td>
-<td><p><cite>HOM_REF</cite></p></td>
-</tr>
-<tr class="row-even"><td><p><cite>*</cite></p></td>
-<td><p>1</p></td>
-<td><p><cite>HET</cite></p></td>
-</tr>
-<tr class="row-odd"><td><p><cite>*</cite></p></td>
-<td><p>2</p></td>
-<td><p><cite>BIALLELIC_ALT</cite></p></td>
-</tr>
-<tr class="row-even"><td><p><cite>*</cite></p></td>
-<td><p><span class="math notranslate nohighlight">\(\ge 3\)</span></p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
-</tr>
-<tr class="row-odd"><td rowspan="3"><p>X-linked dominant</p></td>
-<td><p><cite>*</cite></p></td>
-<td><p>0</p></td>
-<td><p><cite>HOM_REF</cite></p></td>
-</tr>
-<tr class="row-even"><td><p><cite>*</cite></p></td>
-<td><p>1</p></td>
-<td><p><cite>HET</cite></p></td>
-</tr>
-<tr class="row-odd"><td><p><cite>*</cite></p></td>
-<td><p><span class="math notranslate nohighlight">\(\ge 2\)</span></p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
-</tr>
-<tr class="row-even"><td rowspan="6"><p>X-linked recessive</p></td>
-<td><p><cite>*</cite></p></td>
-<td><p>0</p></td>
-<td><p><cite>HOM_REF</cite></p></td>
-</tr>
-<tr class="row-odd"><td rowspan="3"><p><a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Sex.FEMALE" title="gpsea.model.Sex.FEMALE"><code class="xref py py-class docutils literal notranslate"><span class="pre">FEMALE</span></code></a></p></td>
-<td><p>1</p></td>
-<td><p><cite>HET</cite></p></td>
-</tr>
-<tr class="row-even"><td><p>2</p></td>
-<td><p><cite>BIALLELIC_ALT</cite></p></td>
-</tr>
-<tr class="row-odd"><td><p><span class="math notranslate nohighlight">\(\ge 3\)</span></p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
-</tr>
-<tr class="row-even"><td rowspan="2"><p><a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Sex.MALE" title="gpsea.model.Sex.MALE"><code class="xref py py-class docutils literal notranslate"><span class="pre">MALE</span></code></a></p></td>
-<td><p>1</p></td>
-<td><p><cite>HEMI</cite></p></td>
-</tr>
-<tr class="row-odd"><td><p><span class="math notranslate nohighlight">\(\ge 2\)</span></p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
-</tr>
-</tbody>
-</table>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p><cite>BIALLELIC_ALT</cite> includes both homozygous and compound heterozygous genotypes.</p>
-</div>
-<p>Clinical judgment should be used to choose the MoI for the cohort analysis.
-Then a predicate for the desired MoI can be created by one of
-<a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModeOfInheritancePredicate</span></code></a> static constructors:</p>
-<ul class="simple">
-<li><p><a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_dominant"><code class="xref py py-func docutils literal notranslate"><span class="pre">autosomal_dominant()</span></code></a></p></li>
-<li><p><a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive"><code class="xref py py-func docutils literal notranslate"><span class="pre">autosomal_recessive()</span></code></a></p></li>
-<li><p><a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_dominant"><code class="xref py py-func docutils literal notranslate"><span class="pre">x_dominant()</span></code></a></p></li>
-<li><p><a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.x_recessive"><code class="xref py py-func docutils literal notranslate"><span class="pre">x_recessive()</span></code></a></p></li>
+<p>All GPSEA analyses need at least one predicate (typically a <em>genotype</em> predicate) and many require both <em>genotype</em> and <em>phenotype</em> predicates.
+The following pages provide more information.</p>
+<div class="toctree-wrapper compound">
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="predicates/phenotype_predicates.html">Phenotype Predicates</a></li>
+<li class="toctree-l1"><a class="reference internal" href="predicates/genotype_predicates.html">Genotype Predicates</a></li>
 </ul>
-<p>All constructors take an instance
-of <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> as an argument.</p>
-<section id="example">
-<h4>Example<a class="headerlink" href="#example" title="Link to this heading"></a></h4>
-<p>Here we show seting up a predicate for grouping individuals based on
-having a variant that leads to a frameshift or to a stop gain to a fictional transcript <code class="docutils literal notranslate"><span class="pre">NM_1234.5</span></code>
-to test differences between the genotypes of a disease with an autosomal recessive MoI.</p>
-<p>First, we set up a <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a>
-for testing if a variant meets the condition:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_1234.5&#39;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">is_frameshift_or_stop_gain</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span> \
-<span class="gp">... </span>    <span class="o">|</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_GAINED</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">is_frameshift_or_stop_gain</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
-<span class="go">&#39;(FRAMESHIFT_VARIANT on NM_1234.5 OR STOP_GAINED on NM_1234.5)&#39;</span>
-</pre></div>
 </div>
-<p>Next, we use <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive"><code class="xref py py-class docutils literal notranslate"><span class="pre">autosomal_recessive</span></code></a>
-for assigning a patient into a genotype group:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">ModeOfInheritancePredicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">autosomal_recessive</span><span class="p">(</span><span class="n">is_frameshift_or_stop_gain</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Which genotype group does the patient fit in: HOM_REF, HET, BIALLELIC_ALT&#39;</span>
-</pre></div>
-</div>
-<p>The <cite>gt_predicate</cite> can be used in downstream analysis, such as in :class:</p>
-</section>
-</section>
-<section id="filtering-predicate">
-<span id="id3"></span><h3>Filtering predicate<a class="headerlink" href="#filtering-predicate" title="Link to this heading"></a></h3>
-<p>Sometimes a predicate can bin individuals into more genotype groups than necessary and there may be need
-to consider only a subset of the groups. A <cite>GenotypePolyPredicate</cite>
-created by <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.filtering_predicate" title="gpsea.analysis.predicate.genotype.filtering_predicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">filtering_predicate</span></code></a> can retain only a subset
-of the target categorizations of interest.</p>
-<section id="id4">
-<h4>Example<a class="headerlink" href="#id4" title="Link to this heading"></a></h4>
-<p>Let’s suppose we want test the genotype-phenotype association between variants
-that lead to frameshift or a stop gain in a fictional transcript <cite>NM_1234.5</cite>,
-and we are specifically interested in comparing the heterozygous variants
-in a biallelic alternative allele genotypes (homozygous alternate and compound heterozygous).</p>
-<p>First, we set up a <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a>
-for testing if a variant introduces a premature stop codon or leads to the shift of the reading frame:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_1234.5&#39;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">is_frameshift_or_stop_gain</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span> \
-<span class="gp">... </span>    <span class="o">|</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_GAINED</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">is_frameshift_or_stop_gain</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
-<span class="go">&#39;(FRAMESHIFT_VARIANT on NM_1234.5 OR STOP_GAINED on NM_1234.5)&#39;</span>
-</pre></div>
-</div>
-<p>Then, we create <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive" title="gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate.autosomal_recessive"><code class="xref py py-class docutils literal notranslate"><span class="pre">autosomal_recessive</span></code></a>
-to bin according to a genotype group:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">ModeOfInheritancePredicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">autosomal_recessive</span><span class="p">(</span><span class="n">is_frameshift_or_stop_gain</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Which genotype group does the patient fit in: HOM_REF, HET, BIALLELIC_ALT&#39;</span>
-</pre></div>
-</div>
-<p>We see that the <cite>gt_predicate</cite> bins the patients into three groups:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">cats</span> <span class="o">=</span> <span class="n">gt_predicate</span><span class="o">.</span><span class="n">get_categorizations</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">cats</span>
-<span class="go">(Categorization(category=HOM_REF), Categorization(category=HET), Categorization(category=BIALLELIC_ALT))</span>
-</pre></div>
-</div>
-<p>We wrap the categorizations of interest along with the <cite>gt_predicate</cite> by the <cite>filtering_predicate</cite> function,
-and we will get a <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype.GenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a>
-that includes only the categories of interest:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">filtering_predicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">fgt_predicate</span> <span class="o">=</span> <span class="n">filtering_predicate</span><span class="p">(</span>
-<span class="gp">... </span>    <span class="n">predicate</span><span class="o">=</span><span class="n">gt_predicate</span><span class="p">,</span>
-<span class="gp">... </span>    <span class="n">targets</span><span class="o">=</span><span class="p">(</span><span class="n">cats</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">cats</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
-<span class="gp">... </span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">fgt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Which genotype group does the patient fit in: HET, BIALLELIC_ALT&#39;</span>
-</pre></div>
-</div>
-</section>
-</section>
-<section id="groups-predicate">
-<span id="id5"></span><h3>Groups predicate<a class="headerlink" href="#groups-predicate" title="Link to this heading"></a></h3>
-<p>Sometimes, all we want is to compare if there is a difference between individuals
-who include one or more alleles of variant $X$ vs. individuals with variants $Y$,
-vs. individuals with variants $Z$, where $X$, $Y$ and $Z$ are variant predicates.
-We can do this with a <em>groups</em> predicate.</p>
-<p>The <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.groups_predicate" title="gpsea.analysis.predicate.genotype.groups_predicate"><code class="xref py py-func docutils literal notranslate"><span class="pre">groups_predicate()</span></code></a>
-takes <em>n</em> variant predicates and <em>n</em> group labels, and it will assign the patients
-into the respective groups if one or more matching allele is found.
-However, only one predicate is allowed to return a non-zero allele count.
-Otherwise, the patient is assigned with <code class="docutils literal notranslate"><span class="pre">None</span></code> and excluded from the analysis.</p>
-<section id="id6">
-<h4>Example<a class="headerlink" href="#id6" title="Link to this heading"></a></h4>
-<p>Here we show how to build a <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype.GenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a>
-for testing if the individual has at least one missense vs. frameshift vs. synonymous variant.</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span><span class="p">,</span> <span class="n">groups_predicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_1234.5&#39;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">groups_predicate</span><span class="p">(</span>
-<span class="gp">... </span>    <span class="n">predicates</span><span class="o">=</span><span class="p">(</span>
-<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
-<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
-<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">SYNONYMOUS_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
-<span class="gp">... </span>    <span class="p">),</span>
-<span class="gp">... </span>    <span class="n">group_names</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Missense&#39;</span><span class="p">,</span> <span class="s1">&#39;Frameshift&#39;</span><span class="p">,</span> <span class="s1">&#39;Synonymous&#39;</span><span class="p">),</span>
-<span class="gp">... </span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Genotype group: Missense, Frameshift, Synonymous&#39;</span>
-</pre></div>
-</div>
-</section>
-</section>
-<section id="partition-by-the-sex-of-the-individual">
-<span id="sex-predicate"></span><h3>Partition by the sex of the individual<a class="headerlink" href="#partition-by-the-sex-of-the-individual" title="Link to this heading"></a></h3>
-<p>It is easy to investigate the phenotypic differences between females and males.
-The <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.sex_predicate" title="gpsea.analysis.predicate.genotype.sex_predicate"><code class="xref py py-func docutils literal notranslate"><span class="pre">sex_predicate()</span></code></a> provides a predicate
-for partitioning based on the sex of the individual:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">sex_predicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">sex_predicate</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Sex of the individual: FEMALE, MALE&#39;</span>
-</pre></div>
-</div>
-<p>The individuals with <a class="reference internal" href="../apidocs/gpsea.model.html#gpsea.model.Sex.UNKNOWN_SEX" title="gpsea.model.Sex.UNKNOWN_SEX"><code class="xref py py-class docutils literal notranslate"><span class="pre">UNKNOWN_SEX</span></code></a> will be omitted from the analysis.</p>
-</section>
-<section id="partition-by-a-diagnosis">
-<span id="diagnosis-predicate"></span><h3>Partition by a diagnosis<a class="headerlink" href="#partition-by-a-diagnosis" title="Link to this heading"></a></h3>
-<p>It is also possible to bin the individuals based on a diagnosis.
-The <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.diagnosis_predicate" title="gpsea.analysis.predicate.genotype.diagnosis_predicate"><code class="xref py py-func docutils literal notranslate"><span class="pre">diagnosis_predicate()</span></code></a>
-prepares a genotype predicate for assigning an individual into a diagnosis group:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">diagnosis_predicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">diagnosis_predicate</span><span class="p">(</span>
-<span class="gp">... </span>    <span class="n">diagnoses</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;OMIM:154700&#39;</span><span class="p">,</span> <span class="s1">&#39;OMIM:129600&#39;</span><span class="p">),</span>
-<span class="gp">... </span>    <span class="n">labels</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Marfan syndrome&#39;</span><span class="p">,</span> <span class="s1">&#39;Ectopia lentis, familial&#39;</span><span class="p">),</span>
-<span class="gp">... </span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;What disease was diagnosed: OMIM:154700, OMIM:129600&#39;</span>
-</pre></div>
-</div>
-<p>Note, an individual must match only one diagnosis group. Any individuals labeled with two or more diagnoses
-(e.g. an individual with both <em>Marfan syndrome</em> and <em>Ectopia lentis, familial</em>)
-will be automatically omitted from the analysis.</p>
-</section>
-</section>
-<section id="phenotype-predicates">
-<span id="id7"></span><h2>Phenotype predicates<a class="headerlink" href="#phenotype-predicates" title="Link to this heading"></a></h2>
-<p>The phenotype predicate assigns the individual into a group with respect to tested phenotype.
-Typically, the phenotype corresponds to a clinical sign or symptom encoded into an HPO term.</p>
-<section id="propagating-phenotype-predicate">
-<h3>Propagating phenotype predicate<a class="headerlink" href="#propagating-phenotype-predicate" title="Link to this heading"></a></h3>
-<p>When testing for presence or absence of an HPO term, the propagating phenotype predicate
-leverages the <a class="reference internal" href="glossary.html#true-path-rule"><span class="std std-ref">True path rule</span></a> to take advantage of the HPO hierarchy.
-In result, an individual annotated with a term is implicitly annotated with all its ancestors.
-For instance, an individual annotated with <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0001083">Ectopia lentis</a>
-is also annotated with <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000517">Abnormal lens morphology</a>,
-<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0004328">Abnormal anterior eye segment morphology</a>,
-<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0012372">Abnormal eye morphology</a>, …</p>
-<p>Similarly, all descendants of a term, whose presence was specifically excluded in an individual,
-are implicitly excluded.</p>
-<p><a class="reference internal" href="../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate" title="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code></a> implements this logic.</p>
-<section id="id8">
-<h4>Example<a class="headerlink" href="#id8" title="Link to this heading"></a></h4>
-<p>Here we show how to set up <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate" title="gpsea.analysis.predicate.phenotype.PropagatingPhenotypePredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">PropagatingPhenotypePredicate</span></code></a>
-to test for a presence of <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000517">Abnormal lens morphology</a>.</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.phenotype</span> <span class="kn">import</span> <span class="n">PropagatingPhenotypePredicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">query</span> <span class="o">=</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s1">&#39;HP:0000517&#39;</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">pheno_predicate</span> <span class="o">=</span> <span class="n">PropagatingPhenotypePredicate</span><span class="p">(</span>
-<span class="gp">... </span>    <span class="n">hpo</span><span class="o">=</span><span class="n">hpo</span><span class="p">,</span>
-<span class="gp">... </span>    <span class="n">query</span><span class="o">=</span><span class="n">query</span><span class="p">,</span>
-<span class="gp">... </span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">pheno_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Is Abnormal lens morphology present in the patient: Yes, No&#39;</span>
-</pre></div>
-</div>
-<p>TODO: explain <code class="docutils literal notranslate"><span class="pre">missing_implies_phenotype_excluded</span></code></p>
-</section>
-</section>
-<section id="predicates-for-all-cohort-phenotypes">
-<h3>Predicates for all cohort phenotypes<a class="headerlink" href="#predicates-for-all-cohort-phenotypes" title="Link to this heading"></a></h3>
-<p>Constructing phenotype predicates for all HPO terms of a cohort sounds a bit tedious.
-The <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest" title="gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest"><code class="xref py py-func docutils literal notranslate"><span class="pre">prepare_predicates_for_terms_of_interest()</span></code></a>
-function cuts down the tedium:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.phenotype</span> <span class="kn">import</span> <span class="n">prepare_predicates_for_terms_of_interest</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">pheno_predicates</span> <span class="o">=</span> <span class="n">prepare_predicates_for_terms_of_interest</span><span class="p">(</span>
-<span class="gp">... </span>    <span class="n">cohort</span><span class="o">=</span><span class="n">cohort</span><span class="p">,</span>
-<span class="gp">... </span>    <span class="n">hpo</span><span class="o">=</span><span class="n">hpo</span><span class="p">,</span>
-<span class="gp">... </span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">pheno_predicates</span><span class="p">)</span>
-<span class="go">301</span>
-</pre></div>
-</div>
-<p>and prepares predicates for testing 301 HPO terms of the <em>RERE</em> cohort.</p>
-</section>
-</section>
 <section id="gallery">
 <h2>Gallery<a class="headerlink" href="#gallery" title="Link to this heading"></a></h2>
 <p>Here we show examples of predicates used in some of our analyses.</p>
@@ -620,7 +146,7 @@ <h2>Need more?<a class="headerlink" href="#need-more" title="Link to this headin
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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-        <a href="phenotype_predicates.html" class="btn btn-neutral float-right" title="Phenotype Predicates" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="predicates/phenotype_predicates.html" class="btn btn-neutral float-right" title="Phenotype Predicates" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/stable/user-guide/devries.html b/stable/user-guide/predicates/devries.html
similarity index 75%
rename from stable/user-guide/devries.html
rename to stable/user-guide/predicates/devries.html
index 4747c5493..ce402c99d 100644
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+++ b/stable/user-guide/predicates/devries.html
@@ -1,32 +1,32 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en" data-content_root="../../">
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+  <title>De Vries Score &mdash; GPSEA 0.4.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
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-    <script src="../_static/js/html5shiv.min.js"></script>
+    <script src="../../_static/js/html5shiv.min.js"></script>
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-    <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Statistical tests" href="stats.html" />
-    <link rel="prev" title="Phenotype Predicates" href="phenotype_predicates.html" /> 
+        <script src="../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../_static/documentation_options.js?v=6c02275b"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="../../_static/copybutton.js?v=6dbb43f8"></script>
+    <script src="../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" />
+    <link rel="next" title="Genotype Predicates" href="genotype_predicates.html" />
+    <link rel="prev" title="HPO predicate" href="hpo_predicate.html" /> 
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@@ -37,14 +37,14 @@
 
           
           
-          <a href="../index.html" class="icon icon-home">
+          <a href="../../index.html" class="icon icon-home">
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
-  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+  <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
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@@ -53,32 +53,30 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Installation &amp; Tutorial</span></p>
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-<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
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-<li class="toctree-l2 current"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a><ul class="current">
-<li class="toctree-l3 current"><a class="current reference internal" href="#">De Vries Score</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#developmental-delay">Developmental delay</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#prenatal-onset-growth-retardation">Prenatal-onset growth retardation</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#postnatal-growth-abnormalities">Postnatal growth abnormalities</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#facial-dysmorphic-features">Facial dysmorphic features</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#non-facial-dysmorphism-and-congenital-abnormalities">Non-facial dysmorphism and congenital abnormalities</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#final-score">Final score</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#using-the-de-vries-scorer-in-code">Using the De Vries Scorer in code</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../tutorial.html">Tutorial</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../index.html">User guide</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../input-data.html">Input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../exploratory.html">Cohort exploratory analysis</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../predicates.html">Predicates</a><ul class="current">
+<li class="toctree-l3 current"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a><ul class="current">
+<li class="toctree-l4"><a class="reference internal" href="hpo_predicate.html">HPO predicate</a></li>
+<li class="toctree-l4"><a class="reference internal" href="hpo_predicate.html#predicates-for-all-cohort-phenotypes">Predicates for all cohort phenotypes</a></li>
+<li class="toctree-l4 current"><a class="current reference internal" href="#">De Vries Score</a></li>
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 </li>
+<li class="toctree-l3"><a class="reference internal" href="genotype_predicates.html">Genotype Predicates</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../predicates.html#gallery">Gallery</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../predicates.html#need-more">Need more?</a></li>
 </ul>
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-<li class="toctree-l2"><a class="reference internal" href="stats.html">Statistical tests</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="glossary.html">Glossary</a></li>
-<li class="toctree-l2"><a class="reference internal" href="autosomal_recessive.html">Genotype-Phenotype Correlations in Autosomal Recessive Diseases</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../stats.html">Statistical tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../mtc.html">Multiple-testing correction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../glossary.html">Glossary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../autosomal_recessive.html">Genotype-Phenotype Correlations in Autosomal Recessive Diseases</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../apidocs/modules.html">API reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../apidocs/modules.html">API reference</a></li>
 </ul>
 
         </div>
@@ -87,19 +85,20 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../index.html">GPSEA</a>
+          <a href="../../index.html">GPSEA</a>
       </nav>
 
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-      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">User guide</a></li>
+      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../index.html">User guide</a></li>
+          <li class="breadcrumb-item"><a href="../predicates.html">Predicates</a></li>
           <li class="breadcrumb-item"><a href="phenotype_predicates.html">Phenotype Predicates</a></li>
       <li class="breadcrumb-item active">De Vries Score</li>
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-            <a href="../_sources/user-guide/devries.rst.txt" rel="nofollow"> View page source</a>
+            <a href="../../_sources/user-guide/predicates/devries.rst.txt" rel="nofollow"> View page source</a>
       </li>
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   <hr/>
@@ -295,8 +294,8 @@ <h2>Using the De Vries Scorer in code<a class="headerlink" href="#using-the-de-v
            </div>
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-        <a href="stats.html" class="btn btn-neutral float-right" title="Statistical tests" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="hpo_predicate.html" class="btn btn-neutral float-left" title="HPO predicate" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="genotype_predicates.html" class="btn btn-neutral float-right" title="Genotype Predicates" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/stable/user-guide/predicates/diagnosis_predicate.html b/stable/user-guide/predicates/diagnosis_predicate.html
new file mode 100644
index 000000000..27d609c5d
--- /dev/null
+++ b/stable/user-guide/predicates/diagnosis_predicate.html
@@ -0,0 +1,161 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Partition by a diagnosis &mdash; GPSEA 0.4.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
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+        <script src="../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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+    <link rel="next" title="Groups Predicate" href="groups_predicate.html" />
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+</head>
+
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+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../tutorial.html">Tutorial</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../index.html">User guide</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../input-data.html">Input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../exploratory.html">Cohort exploratory analysis</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../predicates.html">Predicates</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
+<li class="toctree-l3 current"><a class="reference internal" href="genotype_predicates.html">Genotype Predicates</a><ul class="current">
+<li class="toctree-l4"><a class="reference internal" href="variant_predicates.html">Variant Predicates</a></li>
+<li class="toctree-l4"><a class="reference internal" href="mode_of_inheritance_predicate.html">Mode of Inheritance Predicates</a></li>
+<li class="toctree-l4"><a class="reference internal" href="male_female_predicate.html">Partition by the sex of the individual</a></li>
+<li class="toctree-l4 current"><a class="current reference internal" href="#">Partition by a diagnosis</a></li>
+<li class="toctree-l4"><a class="reference internal" href="groups_predicate.html">Groups Predicate</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../predicates.html#gallery">Gallery</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../predicates.html#need-more">Need more?</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../stats.html">Statistical tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../mtc.html">Multiple-testing correction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../glossary.html">Glossary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../autosomal_recessive.html">Genotype-Phenotype Correlations in Autosomal Recessive Diseases</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../../apidocs/modules.html">API reference</a></li>
+</ul>
+
+        </div>
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+          <li class="breadcrumb-item"><a href="../index.html">User guide</a></li>
+          <li class="breadcrumb-item"><a href="../predicates.html">Predicates</a></li>
+          <li class="breadcrumb-item"><a href="genotype_predicates.html">Genotype Predicates</a></li>
+      <li class="breadcrumb-item active">Partition by a diagnosis</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../../_sources/user-guide/predicates/diagnosis_predicate.rst.txt" rel="nofollow"> View page source</a>
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+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="partition-by-a-diagnosis">
+<span id="diagnosis-predicate"></span><h1>Partition by a diagnosis<a class="headerlink" href="#partition-by-a-diagnosis" title="Link to this heading"></a></h1>
+<p>It is also possible to bin the individuals based on a diagnosis.
+The <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.diagnosis_predicate" title="gpsea.analysis.predicate.genotype.diagnosis_predicate"><code class="xref py py-func docutils literal notranslate"><span class="pre">diagnosis_predicate()</span></code></a>
+prepares a genotype predicate for assigning an individual into a diagnosis group:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">diagnosis_predicate</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">diagnosis_predicate</span><span class="p">(</span>
+<span class="gp">... </span>    <span class="n">diagnoses</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;OMIM:154700&#39;</span><span class="p">,</span> <span class="s1">&#39;OMIM:129600&#39;</span><span class="p">),</span>
+<span class="gp">... </span>    <span class="n">labels</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Marfan syndrome&#39;</span><span class="p">,</span> <span class="s1">&#39;Ectopia lentis, familial&#39;</span><span class="p">),</span>
+<span class="gp">... </span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
+<span class="go">&#39;What disease was diagnosed: OMIM:154700, OMIM:129600&#39;</span>
+</pre></div>
+</div>
+<p>Note, an individual must match only one diagnosis group. Any individuals labeled with two or more diagnoses
+(e.g. an individual with both <em>Marfan syndrome</em> and <em>Ectopia lentis, familial</em>)
+will be automatically omitted from the analysis.</p>
+</section>
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+<li class="toctree-l3"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Genotype Predicates</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="variant_predicates.html">Variant Predicates</a></li>
+<li class="toctree-l4"><a class="reference internal" href="mode_of_inheritance_predicate.html">Mode of Inheritance Predicates</a></li>
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+<li class="toctree-l4"><a class="reference internal" href="groups_predicate.html">Groups Predicate</a></li>
+</ul>
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+<li class="toctree-l2"><a class="reference internal" href="../autosomal_recessive.html">Genotype-Phenotype Correlations in Autosomal Recessive Diseases</a></li>
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+             
+  <section id="genotype-predicates">
+<span id="id1"></span><h1>Genotype Predicates<a class="headerlink" href="#genotype-predicates" title="Link to this heading"></a></h1>
+<p>A genotype predicate seeks to divide the individuals along an axis that is orthogonal to phenotypes.
+Typically, this includes using the genotype data, such as presence of a missense variant
+in a heterozygous genotype. However, other categorical variables,
+such as diagnoses (TODO - add link to disease predicate) or cluster ids can also be used.</p>
+<p>The genotype predicates test the individual for a presence of variants that meet certain inclusion criteria.
+The testing is done in two steps. First, we count the alleles
+of the matching variants and then we interpret the count, possibly including factors
+such as the expected mode of inheritance and sex, to assign the individual into a group.
+Finding the matching variants is what
+the <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> is all about.</p>
+<div class="toctree-wrapper compound">
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="variant_predicates.html">Variant Predicates</a></li>
+<li class="toctree-l1"><a class="reference internal" href="mode_of_inheritance_predicate.html">Mode of Inheritance Predicates</a></li>
+<li class="toctree-l1"><a class="reference internal" href="male_female_predicate.html">Partition by the sex of the individual</a></li>
+<li class="toctree-l1"><a class="reference internal" href="diagnosis_predicate.html">Partition by a diagnosis</a></li>
+<li class="toctree-l1"><a class="reference internal" href="groups_predicate.html">Groups Predicate</a></li>
+</ul>
+</div>
+</section>
+
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+<li class="toctree-l2 current"><a class="reference internal" href="../predicates.html">Predicates</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
+<li class="toctree-l3 current"><a class="reference internal" href="genotype_predicates.html">Genotype Predicates</a><ul class="current">
+<li class="toctree-l4"><a class="reference internal" href="variant_predicates.html">Variant Predicates</a></li>
+<li class="toctree-l4"><a class="reference internal" href="mode_of_inheritance_predicate.html">Mode of Inheritance Predicates</a></li>
+<li class="toctree-l4"><a class="reference internal" href="male_female_predicate.html">Partition by the sex of the individual</a></li>
+<li class="toctree-l4"><a class="reference internal" href="diagnosis_predicate.html">Partition by a diagnosis</a></li>
+<li class="toctree-l4 current"><a class="current reference internal" href="#">Groups Predicate</a></li>
+</ul>
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+<li class="toctree-l2"><a class="reference internal" href="../glossary.html">Glossary</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../autosomal_recessive.html">Genotype-Phenotype Correlations in Autosomal Recessive Diseases</a></li>
+</ul>
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+          <li class="breadcrumb-item"><a href="../predicates.html">Predicates</a></li>
+          <li class="breadcrumb-item"><a href="genotype_predicates.html">Genotype Predicates</a></li>
+      <li class="breadcrumb-item active">Groups Predicate</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../../_sources/user-guide/predicates/groups_predicate.rst.txt" rel="nofollow"> View page source</a>
+      </li>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="groups-predicate">
+<span id="id1"></span><h1>Groups Predicate<a class="headerlink" href="#groups-predicate" title="Link to this heading"></a></h1>
+<p>Sometimes, all we want is to compare if there is a difference between individuals
+who include one or more alleles of variant <cite>X</cite> vs. individuals with variants <cite>Y</cite>,
+vs. individuals with variants <cite>Z</cite>, where <cite>X</cite>, <cite>Y</cite> and <cite>Z</cite> are variant predicates.
+We can do this with a <em>groups</em> predicate.</p>
+<p>The <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.groups_predicate" title="gpsea.analysis.predicate.genotype.groups_predicate"><code class="xref py py-func docutils literal notranslate"><span class="pre">groups_predicate()</span></code></a>
+takes <em>n</em> variant predicates and <em>n</em> group labels, and it will assign the patients
+into the respective groups if one or more matching allele is found.
+However, only one predicate is allowed to return a non-zero allele count.
+Otherwise, the patient is assigned with <code class="docutils literal notranslate"><span class="pre">None</span></code> and excluded from the analysis.</p>
+<section id="example">
+<h2>Example<a class="headerlink" href="#example" title="Link to this heading"></a></h2>
+<p>Here we show how to build a <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.GenotypePolyPredicate" title="gpsea.analysis.predicate.genotype.GenotypePolyPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenotypePolyPredicate</span></code></a>
+for testing if the individual has at least one missense vs. frameshift vs. synonymous variant.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span><span class="p">,</span> <span class="n">groups_predicate</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_1234.5&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">groups_predicate</span><span class="p">(</span>
+<span class="gp">... </span>    <span class="n">predicates</span><span class="o">=</span><span class="p">(</span>
+<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
+<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
+<span class="gp">... </span>        <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">SYNONYMOUS_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">),</span>
+<span class="gp">... </span>    <span class="p">),</span>
+<span class="gp">... </span>    <span class="n">group_names</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Missense&#39;</span><span class="p">,</span> <span class="s1">&#39;Frameshift&#39;</span><span class="p">,</span> <span class="s1">&#39;Synonymous&#39;</span><span class="p">),</span>
+<span class="gp">... </span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
+<span class="go">&#39;Genotype group: Missense, Frameshift, Synonymous&#39;</span>
+</pre></div>
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+  <section id="hpo-predicate">
+<span id="id1"></span><h1>HPO predicate<a class="headerlink" href="#hpo-predicate" title="Link to this heading"></a></h1>
+<p>When testing for presence or absence of an HPO term, the <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate" title="gpsea.analysis.predicate.phenotype.HpoPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">HpoPredicate</span></code></a>
+leverages the <a class="reference internal" href="../glossary.html#true-path-rule"><span class="std std-ref">True path rule</span></a> to take advantage of the HPO hierarchy.
+In result, an individual annotated with a term is implicitly annotated with all its ancestors.
+For instance, an individual annotated with <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0001083">Ectopia lentis</a>
+is also annotated with <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000517">Abnormal lens morphology</a>,
+<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0004328">Abnormal anterior eye segment morphology</a>,
+<a class="reference external" href="https://hpo.jax.org/browse/term/HP:0012372">Abnormal eye morphology</a>, …</p>
+<p>Similarly, all descendants of a term, whose presence was specifically excluded in an individual,
+are implicitly excluded.</p>
+<section id="example">
+<h2>Example<a class="headerlink" href="#example" title="Link to this heading"></a></h2>
+<p>Here we show how to set up <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.HpoPredicate" title="gpsea.analysis.predicate.phenotype.HpoPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">HpoPredicate</span></code></a>
+to test for a presence of <a class="reference external" href="https://hpo.jax.org/browse/term/HP:0000517">Abnormal lens morphology</a>.</p>
+<p>We need to load <code class="xref py py-class docutils literal notranslate"><span class="pre">MinimalOntology</span></code> with HPO data to access the HPO hierarchy:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">hpotk</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">store</span> <span class="o">=</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">configure_ontology_store</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">hpo</span> <span class="o">=</span> <span class="n">store</span><span class="o">.</span><span class="n">load_minimal_hpo</span><span class="p">(</span><span class="n">release</span><span class="o">=</span><span class="s1">&#39;v2024-07-01&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>and now we can set up a predicate to test for presence of <em>Abnormal lens morphology</em>:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.phenotype</span> <span class="kn">import</span> <span class="n">HpoPredicate</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">query</span> <span class="o">=</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">TermId</span><span class="o">.</span><span class="n">from_curie</span><span class="p">(</span><span class="s1">&#39;HP:0000517&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">pheno_predicate</span> <span class="o">=</span> <span class="n">HpoPredicate</span><span class="p">(</span>
+<span class="gp">... </span>    <span class="n">hpo</span><span class="o">=</span><span class="n">hpo</span><span class="p">,</span>
+<span class="gp">... </span>    <span class="n">query</span><span class="o">=</span><span class="n">query</span><span class="p">,</span>
+<span class="gp">... </span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">pheno_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
+<span class="go">&#39;Is Abnormal lens morphology present in the patient: Yes, No&#39;</span>
+</pre></div>
+</div>
+</section>
+<section id="missing-implies-phenotype-excluded">
+<h2>missing_implies_phenotype_excluded<a class="headerlink" href="#missing-implies-phenotype-excluded" title="Link to this heading"></a></h2>
+<p>In many cases, published reports of clinical data about individuals with rare diseases describes phenotypic features that were observed, but do not
+provide a comprehensive list of features that were explicitly excluded. By default, GPSEA will only include features that are recorded as observed or excluded in a phenopacket.
+Setting this argument to True will cause “n/a” entries to be set to “excluded”. We provide this option for exploration but do not recommend its use for the
+final analysis unless the assumption behind it is known to be true.</p>
+</section>
+</section>
+<section id="predicates-for-all-cohort-phenotypes">
+<h1>Predicates for all cohort phenotypes<a class="headerlink" href="#predicates-for-all-cohort-phenotypes" title="Link to this heading"></a></h1>
+<p>Constructing phenotype predicates for all HPO terms of a cohort sounds a bit tedious.
+The <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.phenotype.html#gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest" title="gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest"><code class="xref py py-func docutils literal notranslate"><span class="pre">prepare_predicates_for_terms_of_interest()</span></code></a>
+function cuts down the tedium.</p>
+<p>For a given phenopacket collection (e.g. 156 patients with mutations in <em>WWOX</em> gene included in Phenopacket Store version <cite>0.1.18</cite>)</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">ppktstore.registry</span> <span class="kn">import</span> <span class="n">configure_phenopacket_registry</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">registry</span> <span class="o">=</span> <span class="n">configure_phenopacket_registry</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">with</span> <span class="n">registry</span><span class="o">.</span><span class="n">open_phenopacket_store</span><span class="p">(</span><span class="n">release</span><span class="o">=</span><span class="s1">&#39;0.1.18&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">ps</span><span class="p">:</span>
+<span class="gp">... </span>    <span class="n">phenopackets</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">iter_cohort_phenopackets</span><span class="p">(</span><span class="s1">&#39;TBX5&#39;</span><span class="p">))</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">)</span>
+<span class="go">156</span>
+</pre></div>
+</div>
+<p>processed into a cohort</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">configure_caching_cohort_creator</span><span class="p">,</span> <span class="n">load_phenopackets</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">cohort_creator</span> <span class="o">=</span> <span class="n">configure_caching_cohort_creator</span><span class="p">(</span><span class="n">hpo</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">cohort</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">load_phenopackets</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">cohort_creator</span><span class="p">)</span>  
+<span class="go">Individuals Processed: ...</span>
+</pre></div>
+</div>
+<p>we can create HPO predicates for testing all 260 HPO terms used in the cohort</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.phenotype</span> <span class="kn">import</span> <span class="n">prepare_predicates_for_terms_of_interest</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">pheno_predicates</span> <span class="o">=</span> <span class="n">prepare_predicates_for_terms_of_interest</span><span class="p">(</span>
+<span class="gp">... </span>    <span class="n">cohort</span><span class="o">=</span><span class="n">cohort</span><span class="p">,</span>
+<span class="gp">... </span>    <span class="n">hpo</span><span class="o">=</span><span class="n">hpo</span><span class="p">,</span>
+<span class="gp">... </span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">pheno_predicates</span><span class="p">)</span>
+<span class="go">260</span>
+</pre></div>
+</div>
+<p>and subject the predicates into further analysis, such as <a class="reference internal" href="../../apidocs/gpsea.analysis.pcats.html#gpsea.analysis.pcats.HpoTermAnalysis" title="gpsea.analysis.pcats.HpoTermAnalysis"><code class="xref py py-class docutils literal notranslate"><span class="pre">HpoTermAnalysis</span></code></a>.</p>
+</section>
+
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+<li class="toctree-l4 current"><a class="current reference internal" href="#">Partition by the sex of the individual</a></li>
+<li class="toctree-l4"><a class="reference internal" href="diagnosis_predicate.html">Partition by a diagnosis</a></li>
+<li class="toctree-l4"><a class="reference internal" href="groups_predicate.html">Groups Predicate</a></li>
+</ul>
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+<li class="toctree-l2"><a class="reference internal" href="../autosomal_recessive.html">Genotype-Phenotype Correlations in Autosomal Recessive Diseases</a></li>
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+             
+  <section id="partition-by-the-sex-of-the-individual">
+<span id="male-female-predicate"></span><h1>Partition by the sex of the individual<a class="headerlink" href="#partition-by-the-sex-of-the-individual" title="Link to this heading"></a></h1>
+<p>It is easy to investigate the phenotypic differences between females and males.
+The <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.sex_predicate" title="gpsea.analysis.predicate.genotype.sex_predicate"><code class="xref py py-func docutils literal notranslate"><span class="pre">sex_predicate()</span></code></a> provides a predicate
+for partitioning based on the sex of the individual:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">sex_predicate</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">sex_predicate</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
+<span class="go">&#39;Sex of the individual: FEMALE, MALE&#39;</span>
+</pre></div>
+</div>
+<p>The individuals with <a class="reference internal" href="../../apidocs/gpsea.model.html#gpsea.model.Sex.UNKNOWN_SEX" title="gpsea.model.Sex.UNKNOWN_SEX"><code class="xref py py-class docutils literal notranslate"><span class="pre">UNKNOWN_SEX</span></code></a> will be omitted from the analysis.</p>
+<p>Note that we have implemented this predicate as a genotype predicate, because it is used in
+place of other genotype predicates. Currently, it is not possible to compare the distribution of genotypes across sexes.</p>
+</section>
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+             
+  <section id="mode-of-inheritance-predicates">
+<span id="mode-of-inheritance-predicate"></span><h1>Mode of Inheritance Predicates<a class="headerlink" href="#mode-of-inheritance-predicates" title="Link to this heading"></a></h1>
+<p>There are five basic modes of inheritance for single-gene diseases: autosomal dominant,
+autosomal recessive, X-linked dominant, X-linked recessive, and mitochondrial
+(See <a class="reference external" href="https://www.ncbi.nlm.nih.gov/books/NBK132145/">Understanding Genetics, Appendix B</a>).</p>
+<p>The <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_dominant" title="gpsea.analysis.predicate.genotype.autosomal_dominant"><code class="xref py py-class docutils literal notranslate"><span class="pre">autosomal_dominant</span></code></a>
+and <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_recessive" title="gpsea.analysis.predicate.genotype.autosomal_recessive"><code class="xref py py-class docutils literal notranslate"><span class="pre">autosomal_recessive</span></code></a>
+assigns the individual into a group based on the number of the alleles
+observed in the individual.
+GPSEA supports the following Mendelian modes of inheritance (MoI):</p>
+<table class="docutils align-default">
+<thead>
+<tr class="row-odd"><th class="head"><p>Mode of inheritance</p></th>
+<th class="head"><p>Allele count</p></th>
+<th class="head"><p>Genotype category</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td rowspan="3"><p>Autosomal dominant</p></td>
+<td><p>0</p></td>
+<td><p><cite>HOM_REF</cite></p></td>
+</tr>
+<tr class="row-odd"><td><p>1</p></td>
+<td><p><cite>HET</cite></p></td>
+</tr>
+<tr class="row-even"><td><p><span class="math notranslate nohighlight">\(\ge 2\)</span></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
+</tr>
+<tr class="row-odd"><td rowspan="4"><p>Autosomal recessive</p></td>
+<td><p>0</p></td>
+<td><p><cite>HOM_REF</cite></p></td>
+</tr>
+<tr class="row-even"><td><p>1</p></td>
+<td><p><cite>HET</cite></p></td>
+</tr>
+<tr class="row-odd"><td><p>2</p></td>
+<td><p><cite>BIALLELIC_ALT</cite></p></td>
+</tr>
+<tr class="row-even"><td><p><span class="math notranslate nohighlight">\(\ge 3\)</span></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">None</span></code></p></td>
+</tr>
+</tbody>
+</table>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p><cite>BIALLELIC_ALT</cite> includes both homozygous and compound heterozygous genotypes.</p>
+</div>
+<p>Clinical judgment should be used to choose the MoI for the cohort analysis.
+Then a predicate for the desired MoI can be created by calling one
+of the following methods:</p>
+<ul class="simple">
+<li><p><a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_dominant" title="gpsea.analysis.predicate.genotype.autosomal_dominant"><code class="xref py py-func docutils literal notranslate"><span class="pre">autosomal_dominant()</span></code></a></p></li>
+<li><p><a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_recessive" title="gpsea.analysis.predicate.genotype.autosomal_recessive"><code class="xref py py-func docutils literal notranslate"><span class="pre">autosomal_recessive()</span></code></a></p></li>
+</ul>
+<p>By default, the MoI predicates will use <em>all</em> variants recorded in the individual.
+However, a <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a>
+can be provided to select a variant subset, if necessary.</p>
+<section id="assign-individuals-into-genotype-groups">
+<h2>Assign individuals into genotype groups<a class="headerlink" href="#assign-individuals-into-genotype-groups" title="Link to this heading"></a></h2>
+<p>Here we show seting up a predicate for grouping individuals for differences
+between genotypes of a disease with an autosomal recessive MoI.</p>
+<p>We use <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.autosomal_recessive" title="gpsea.analysis.predicate.genotype.autosomal_recessive"><code class="xref py py-class docutils literal notranslate"><span class="pre">autosomal_recessive</span></code></a>
+to create the predicate:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">autosomal_recessive</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">autosomal_recessive</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
+<span class="go">&#39;What is the genotype group: HOM_REF, HET, BIALLELIC_ALT&#39;</span>
+</pre></div>
+</div>
+<p>The predicate will use <em>all</em> recorded variants to determine if the individual belongs into
+homozygous reference (<cite>HOM_REF</cite>), heterozygous (<cite>HET</cite>), or biallelic alternative (<cite>BIALLELIC_ALT</cite>)
+category.</p>
+</section>
+<section id="use-a-subset-of-variants-for-choosing-the-genotype-group">
+<h2>Use a subset of variants for choosing the genotype group<a class="headerlink" href="#use-a-subset-of-variants-for-choosing-the-genotype-group" title="Link to this heading"></a></h2>
+<p>To select specific variants, a <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a>
+can be registered with the MoI predicate.
+For instance, the following can be done to only consider the variants that lead
+to a missense change on a fictional transcript <code class="docutils literal notranslate"><span class="pre">NM_1234.5</span></code>
+when assigning the genotype group. We set up the variant predicate:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_1234.5&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">is_missense</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">is_missense</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
+<span class="go">&#39;MISSENSE_VARIANT on NM_1234.5&#39;</span>
+</pre></div>
+</div>
+<p>and we use it to create the MoI predicate:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">autosomal_recessive</span><span class="p">(</span><span class="n">is_missense</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
+<span class="go">&#39;What is the genotype group: HOM_REF, HET, BIALLELIC_ALT&#39;</span>
+</pre></div>
+</div>
+</section>
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="variant_predicates.html" class="btn btn-neutral float-left" title="Variant Predicates" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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+  <section id="phenotype-predicates">
+<span id="id1"></span><h1>Phenotype Predicates<a class="headerlink" href="#phenotype-predicates" title="Link to this heading"></a></h1>
+<p>GPSEA offers several phenotype predicates.</p>
+<p>TODO – separate explanations for HPO (Fisher), scores (Mann Whitney) and survival (log rank test).</p>
+<div class="toctree-wrapper compound">
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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+<li class="toctree-l1"><a class="reference internal" href="hpo_predicate.html">HPO predicate</a></li>
+<li class="toctree-l1"><a class="reference internal" href="hpo_predicate.html#predicates-for-all-cohort-phenotypes">Predicates for all cohort phenotypes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="devries.html">De Vries Score</a></li>
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+             
+  <section id="variant-predicates">
+<span id="id1"></span><h1>Variant Predicates<a class="headerlink" href="#variant-predicates" title="Link to this heading"></a></h1>
+<p>GPSEA uses the <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a> class
+to test if a <a class="reference internal" href="../../apidocs/gpsea.model.html#gpsea.model.Variant" title="gpsea.model.Variant"><code class="xref py py-class docutils literal notranslate"><span class="pre">Variant</span></code></a> meets the inclusion criteria.
+The variant predicate can leverage multiple primary data:</p>
+<table class="docutils align-default">
+<thead>
+<tr class="row-odd"><th class="head"><p>Primary data source</p></th>
+<th class="head"><p>Example</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>Allele</p></td>
+<td><p>the variant being a deletion or a single nucleotide variant (SNV)</p></td>
+</tr>
+<tr class="row-odd"><td><p>Genome</p></td>
+<td><p>overlaps of a target genomic region</p></td>
+</tr>
+<tr class="row-even"><td><p>Functional annotation</p></td>
+<td><p>variant is predicted to lead to a missense change or affect an exon of certain transcript</p></td>
+</tr>
+<tr class="row-odd"><td><p>Protein data</p></td>
+<td><p>variant is located in a region encoding a protein domain, protein feature type</p></td>
+</tr>
+</tbody>
+</table>
+<p>which demands a considerable amount of flexibility for creating the predicate.</p>
+<p>As a rule of thumb, the predicates for testing basic conditions are available off the shelf,
+and they can be used as building block for testing for more complex conditions,
+such as testing if the variant is “a missense or synonymous variant located in exon 6 of transcript <cite>NM_013275.6</cite>”.</p>
+<p>Let’s demonstrate this on few examples.
+We will load a cohort of 19 subjects with variants in <em>RERE</em>,
+leading to <a class="reference external" href="https://omim.org/entry/142900">Holt-Oram syndrome MIM:142900</a>.
+The the clinical signs and symptoms of the subjects were encoded into HPO terms
+along with the pathogenic <em>RERE</em> variant.</p>
+<p>Let’s load the phenopackets, as previously described in greater detail the <a class="reference internal" href="../input-data.html#input-data"><span class="std std-ref">Input data</span></a> section.
+Briefly, we first load HPO:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">hpotk</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">store</span> <span class="o">=</span> <span class="n">hpotk</span><span class="o">.</span><span class="n">configure_ontology_store</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">hpo</span> <span class="o">=</span> <span class="n">store</span><span class="o">.</span><span class="n">load_minimal_hpo</span><span class="p">(</span><span class="n">release</span><span class="o">=</span><span class="s1">&#39;v2024-07-01&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>then, we configure the cohort creator:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">configure_caching_cohort_creator</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">cohort_creator</span> <span class="o">=</span> <span class="n">configure_caching_cohort_creator</span><span class="p">(</span><span class="n">hpo</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>which we use to create a <a class="reference internal" href="../../apidocs/gpsea.model.html#gpsea.model.Cohort" title="gpsea.model.Cohort"><code class="xref py py-class docutils literal notranslate"><span class="pre">Cohort</span></code></a> from a bunch of phenopackets
+from the release <cite>0.1.18</cite> of <a class="reference external" href="https://github.com/monarch-initiative/phenopacket-store">Phenopacket Store</a>.
+We will load 19 individuals with mutations in <em>RERE</em> gene:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">ppktstore.registry</span> <span class="kn">import</span> <span class="n">configure_phenopacket_registry</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">registry</span> <span class="o">=</span> <span class="n">configure_phenopacket_registry</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">with</span> <span class="n">registry</span><span class="o">.</span><span class="n">open_phenopacket_store</span><span class="p">(</span><span class="n">release</span><span class="o">=</span><span class="s1">&#39;0.1.18&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">ps</span><span class="p">:</span>
+<span class="gp">... </span>    <span class="n">phenopackets</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">iter_cohort_phenopackets</span><span class="p">(</span><span class="s1">&#39;RERE&#39;</span><span class="p">))</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">)</span>
+<span class="go">19</span>
+</pre></div>
+</div>
+<p>and we will convert the phenopacket into a <a class="reference internal" href="../../apidocs/gpsea.model.html#gpsea.model.Cohort" title="gpsea.model.Cohort"><code class="xref py py-class docutils literal notranslate"><span class="pre">Cohort</span></code></a>:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">load_phenopackets</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">cohort</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">load_phenopackets</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">cohort_creator</span><span class="p">)</span>  
+<span class="go">Individuals Processed: ...</span>
+</pre></div>
+</div>
+<p>To demonstrate the predicate API, we will use the variant <code class="docutils literal notranslate"><span class="pre">1_8358231_8358231_T_C</span></code> that corresponds
+to a pathogenic variant <a class="reference external" href="https://www.ncbi.nlm.nih.gov/clinvar/variation/522858/">VCV000522858.5</a>
+that replaces the histidine encoded by the 1435th codon of <cite>NM_001042681.2</cite> with arginine: <code class="docutils literal notranslate"><span class="pre">NM_001042681.2(RERE):c.4304A&gt;G</span> <span class="pre">(p.His1435Arg)</span></code>.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">variant_key_of_interest</span> <span class="o">=</span> <span class="s1">&#39;1_8358231_8358231_T_C&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">variant</span> <span class="o">=</span> <span class="n">cohort</span><span class="o">.</span><span class="n">get_variant_by_key</span><span class="p">(</span><span class="n">variant_key_of_interest</span><span class="p">)</span>
+</pre></div>
+</div>
+<section id="building-blocks">
+<h2>Building blocks<a class="headerlink" href="#building-blocks" title="Link to this heading"></a></h2>
+<p>We can check that the variant overlaps with <em>RERE</em>:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gene</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">gene</span><span class="p">(</span><span class="s1">&#39;RERE&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gene</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+<span class="go">True</span>
+</pre></div>
+</div>
+<p>it overlaps with the <em>MANE</em> transcript:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">rere_mane_tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_001042681.2&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">tx</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">transcript</span><span class="p">(</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">tx</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+<span class="go">True</span>
+</pre></div>
+</div>
+<p>it in fact overlaps with the exon 20:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">exon20</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">exon</span><span class="p">(</span><span class="n">exon</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">exon20</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+<span class="go">True</span>
+</pre></div>
+</div>
+<p>and leads to a missense mutation with respect to the MANE transcript:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">missense</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">missense</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+<span class="go">True</span>
+</pre></div>
+</div>
+<p>See <a class="reference internal" href="../../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicates" title="gpsea.analysis.predicate.genotype.VariantPredicates"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicates</span></code></a>
+for more info on the predicates available off the shelf.</p>
+</section>
+<section id="complex-conditions">
+<h2>Complex conditions<a class="headerlink" href="#complex-conditions" title="Link to this heading"></a></h2>
+<p>We can combine the building blocks to test for more elaborate conditions.
+For instance, we can test if the variant meets <em>any</em> or several conditions:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">nonsense</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">STOP_GAINED</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">missense_or_nonsense</span> <span class="o">=</span> <span class="n">missense</span> <span class="o">|</span> <span class="n">nonsense</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">missense_or_nonsense</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+<span class="go">True</span>
+</pre></div>
+</div>
+<p>or <em>all</em> conditions:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">missense_and_exon20</span> <span class="o">=</span> <span class="n">missense</span> <span class="o">&amp;</span> <span class="n">exon20</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">missense_and_exon20</span><span class="o">.</span><span class="n">test</span><span class="p">(</span><span class="n">variant</span><span class="p">)</span>
+<span class="go">True</span>
+</pre></div>
+</div>
+<p>The <cite>VariantPredicate</cite> overloads Python <code class="docutils literal notranslate"><span class="pre">&amp;</span></code> (AND) and <code class="docutils literal notranslate"><span class="pre">|</span></code> (OR) operators to build a compound predicate from lower level building blocks.</p>
+<p>Therefore, there is nothing that prevents us to combine the predicates into multi-level tests,
+such as testing if the variant is a <em>“chromosomal deletion” or a deletion which removes at least 50 bp</em>:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantClass</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">chromosomal_deletion</span> <span class="o">=</span> <span class="s2">&quot;SO:1000029&quot;</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">predicate</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">structural_type</span><span class="p">(</span><span class="n">chromosomal_deletion</span><span class="p">)</span> <span class="o">|</span> <span class="p">(</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_class</span><span class="p">(</span><span class="n">VariantClass</span><span class="o">.</span><span class="n">DEL</span><span class="p">)</span> <span class="o">&amp;</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">change_length</span><span class="p">(</span><span class="s2">&quot;&lt;=&quot;</span><span class="p">,</span> <span class="o">-</span><span class="mi">50</span><span class="p">))</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">predicate</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
+<span class="go">&#39;(structural type is SO:1000029 OR (variant class is DEL AND change length &lt;= -50))&#39;</span>
+</pre></div>
+</div>
+</section>
+<section id="inverting-conditions">
+<h2>Inverting conditions<a class="headerlink" href="#inverting-conditions" title="Link to this heading"></a></h2>
+<p>Sometimes we may want to test the variant for a condition that must <em>not</em> be met.
+For instance, we may want to test if the variant is a deletion
+that is <em>not</em> predicted to shift the transcript reading frame.
+One of doing this would be to build a compound predicates
+for all variant effects except of <a class="reference internal" href="../../apidocs/gpsea.model.html#gpsea.model.VariantEffect.FRAMESHIFT_VARIANT" title="gpsea.model.VariantEffect.FRAMESHIFT_VARIANT"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRAMESHIFT_VARIANT</span></code></a>:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_effects</span> <span class="o">=</span> <span class="p">(</span>
+<span class="gp">... </span>  <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SYNONYMOUS_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">MISSENSE_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INTRON_VARIANT</span><span class="p">,</span>
+<span class="gp">... </span>  <span class="c1"># and many more effects..</span>
+<span class="gp">... </span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_predicate</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">eff</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span> <span class="k">for</span> <span class="n">eff</span> <span class="ow">in</span> <span class="n">non_frameshift_effects</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>However, this is clearly tedious and it would be much better implemented
+by a simple logical not of a predicate for a frameshift variant effect.</p>
+<p>To support this, <cite>VariantPredicate</cite> implements <em>logical inversion</em>
+which corresponds to Python’s <code class="docutils literal notranslate"><span class="pre">~</span></code> operator (tilde), to wrap
+the underlying predicate and to invert its test result.</p>
+<p>This is how we can use the predicate inversion to build the predicate for non-frameshift deletions:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_del</span> <span class="o">=</span> <span class="o">~</span><span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="o">=</span><span class="n">rere_mane_tx_id</span><span class="p">)</span> <span class="o">&amp;</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_class</span><span class="p">(</span><span class="n">VariantClass</span><span class="o">.</span><span class="n">DEL</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">non_frameshift_del</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
+<span class="go">&#39;(NOT FRAMESHIFT_VARIANT on NM_001042681.2 AND variant class is DEL)&#39;</span>
+</pre></div>
+</div>
+<p>Note the presence of a tilde <code class="docutils literal notranslate"><span class="pre">~</span></code> before the variant effect predicate and resulting <code class="docutils literal notranslate"><span class="pre">NOT</span></code> in the predicate question.</p>
+<p>The variant predicate offers a flexible API for testing if variants meet a condition.
+However, the genotype phenotype correlations are done on the individual level
+and the variant predicates are used as a component of the genotype predicate.
+The next sections show how to use variant predicates to assign individuals into groups.</p>
+</section>
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="genotype_predicates.html" class="btn btn-neutral float-left" title="Genotype Predicates" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="mode_of_inheritance_predicate.html" class="btn btn-neutral float-right" title="Mode of Inheritance Predicates" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
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diff --git a/stable/user-guide/stats.html b/stable/user-guide/stats.html
index 6ae3e4f9e..c805acf29 100644
--- a/stable/user-guide/stats.html
+++ b/stable/user-guide/stats.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Statistical tests &mdash; GPSEA 0.3.0 documentation</title>
+  <title>Statistical tests &mdash; GPSEA 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -17,7 +17,7 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=e259d695"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -28,7 +28,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Multiple-testing correction" href="mtc.html" />
-    <link rel="prev" title="De Vries Score" href="devries.html" /> 
+    <link rel="prev" title="Groups Predicate" href="predicates/groups_predicate.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -43,7 +43,7 @@
             GPSEA
           </a>
               <div class="version">
-                0.3
+                0.4
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -61,7 +61,6 @@
 <li class="toctree-l2"><a class="reference internal" href="input-data.html">Input data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="exploratory.html">Cohort exploratory analysis</a></li>
 <li class="toctree-l2"><a class="reference internal" href="predicates.html">Predicates</a></li>
-<li class="toctree-l2"><a class="reference internal" href="phenotype_predicates.html">Phenotype Predicates</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Statistical tests</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#compare-genotype-and-phenotype-groups">Compare genotype and phenotype groups</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="#fisher-exact-test-fet">Fisher exact test (FET)</a></li>
@@ -184,7 +183,7 @@ <h5>Create cohort<a class="headerlink" href="#create-cohort" title="Link to this
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">configure_caching_cohort_creator</span><span class="p">,</span> <span class="n">load_phenopackets</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">cohort_creator</span> <span class="o">=</span> <span class="n">configure_caching_cohort_creator</span><span class="p">(</span><span class="n">hpo</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">cohort</span><span class="p">,</span> <span class="n">qc_results</span> <span class="o">=</span> <span class="n">load_phenopackets</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">cohort_creator</span><span class="p">)</span>  
-<span class="go">Patients Created: ...</span>
+<span class="go">Individuals Processed: ...</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">qc_results</span><span class="o">.</span><span class="n">summarize</span><span class="p">()</span>  
 <span class="go">Validated under none policy</span>
 <span class="go">No errors or warnings were found</span>
@@ -205,7 +204,7 @@ <h5>Configure analysis<a class="headerlink" href="#configure-analysis" title="Li
 First, we create a <a class="reference internal" href="../apidocs/gpsea.analysis.predicate.genotype.html#gpsea.analysis.predicate.genotype.VariantPredicate" title="gpsea.analysis.predicate.genotype.VariantPredicate"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantPredicate</span></code></a>
 to test if the variant leads to a frameshift (in this case):</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.model</span> <span class="kn">import</span> <span class="n">VariantEffect</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span><span class="p">,</span> <span class="n">boolean_predicate</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">VariantPredicates</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tx_id</span> <span class="o">=</span> <span class="s1">&#39;NM_181486.4&#39;</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">is_frameshift</span> <span class="o">=</span> <span class="n">VariantPredicates</span><span class="o">.</span><span class="n">variant_effect</span><span class="p">(</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">FRAMESHIFT_VARIANT</span><span class="p">,</span> <span class="n">tx_id</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">is_frameshift</span><span class="o">.</span><span class="n">get_question</span><span class="p">()</span>
@@ -214,10 +213,10 @@ <h5>Configure analysis<a class="headerlink" href="#configure-analysis" title="Li
 </div>
 <p>and then we choose the expected mode of inheritance to test. In case of <em>TBX5</em>,
 we expect the autosomal dominant mode of inheritance:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">ModeOfInheritancePredicate</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">ModeOfInheritancePredicate</span><span class="o">.</span><span class="n">autosomal_dominant</span><span class="p">(</span><span class="n">is_frameshift</span><span class="p">)</span>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate.genotype</span> <span class="kn">import</span> <span class="n">autosomal_dominant</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span> <span class="o">=</span> <span class="n">autosomal_dominant</span><span class="p">(</span><span class="n">is_frameshift</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">gt_predicate</span><span class="o">.</span><span class="n">display_question</span><span class="p">()</span>
-<span class="go">&#39;Which genotype group does the patient fit in: HOM_REF, HET&#39;</span>
+<span class="go">&#39;What is the genotype group: HOM_REF, HET&#39;</span>
 </pre></div>
 </div>
 <p><cite>gt_predicate</cite> will assign the patients with no frameshift variant allele into <cite>HOM_REF</cite> group
@@ -226,7 +225,7 @@ <h5>Configure analysis<a class="headerlink" href="#configure-analysis" title="Li
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <p>Mode of inheritance testing is not the only way to dissect by a genotype.
-See the <a class="reference internal" href="predicates.html#genotype-predicates"><span class="std std-ref">Genotype predicates</span></a> section for more info.</p>
+See the <a class="reference internal" href="predicates/genotype_predicates.html#genotype-predicates"><span class="std std-ref">Genotype Predicates</span></a> section for more info.</p>
 </div>
 <p><strong>Phenotype predicates</strong></p>
 <p>We recommend testing the genotype phenotype association for all HPO terms that are present in 2 or more cohort members,
@@ -295,10 +294,10 @@ <h5>Analysis<a class="headerlink" href="#analysis" title="Link to this heading">
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span>
 <span class="go">260</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">result</span><span class="o">.</span><span class="n">total_tests</span>
-<span class="go">17</span>
+<span class="go">16</span>
 </pre></div>
 </div>
-<p>Thanks to Phenotype MTC filter, we only tested 17 out of 260 terms.
+<p>Thanks to Phenotype MTC filter, we only tested 16 out of 260 terms.
 We can learn more by showing the MTC filter report:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.view</span> <span class="kn">import</span> <span class="n">MtcStatsViewer</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">mtc_viewer</span> <span class="o">=</span> <span class="n">MtcStatsViewer</span><span class="p">()</span>
@@ -357,9 +356,9 @@ <h5>Analysis<a class="headerlink" href="#analysis" title="Link to this heading">
   <h1>Phenotype testing report</h1>
   <p>Phenotype MTC filter: <em>HPO MTC filter</em></p>
   <p>Multiple testing correction: <em>fdr_bh</em></p>
-  <p>Performed statistical tests for 17 out of the total of 260 HPO terms.</p>
+  <p>Performed statistical tests for 16 out of the total of 260 HPO terms.</p>
     <table>
-      <caption>Using <em>HPO MTC filter</em>, 243 term(s) were omitted from statistical analysis.</caption>
+      <caption>Using <em>HPO MTC filter</em>, 244 term(s) were omitted from statistical analysis.</caption>
         <tbody>
           <tr>
             <th>Code</th>
@@ -368,80 +367,45 @@ <h1>Phenotype testing report</h1>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 2 observations (not powered for 2x2)</td>
-            <td>51</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term because all genotypes have same HPO observed proportions</td>
-            <td>50</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping general term</td>
-            <td>44</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 3 observations (not powered for 2x2)</td>
-            <td>27</td>
-          </tr>
-          
-          <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 6 observations (not powered for 2x2)</td>
-            <td>19</td>
+            <td>HMF01</td>
+            <td>Skipping term with maximum frequency that was less than threshold 0.2</td>
+            <td>10</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 4 observations (not powered for 2x2)</td>
-            <td>16</td>
+            <td>HMF02</td>
+            <td>Skipping term because no genotype has more than one observed HPO count</td>
+            <td>4</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 5 observations (not powered for 2x2)</td>
-            <td>10</td>
+            <td>HMF03</td>
+            <td>Skipping term because of a child term with the same individual counts</td>
+            <td>1</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with maximum frequency that was less than threshold 0.2</td>
-            <td>10</td>
+            <td>HMF04</td>
+            <td>Skipping term because all genotypes have same HPO observed proportions</td>
+            <td>50</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term with only 1 observations (not powered for 2x2)</td>
-            <td>7</td>
+            <td>HMF05</td>
+            <td>Skipping term because one genotype had zero observations</td>
+            <td>5</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term because one genotype had zero observations</td>
-            <td>5</td>
+            <td>HMF06</td>
+            <td>Skipping term with less than 7 observations (not powered for 2x2)</td>
+            <td>130</td>
           </tr>
           
           <tr>
-            <!-- TODO: plug the real reason code here -->
-            <td>TODO</td>
-            <td>Skipping term because no genotype has more than one observed HPO count</td>
-            <td>4</td>
+            <td>HMF08</td>
+            <td>Skipping general term</td>
+            <td>44</td>
           </tr>
           
         </tbody>
@@ -452,17 +416,16 @@ <h1>Phenotype testing report</h1>
 <section id="genotype-phenotype-associations">
 <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenotype-associations" title="Link to this heading"></a></h5>
 <p>Last, let’s explore the associations. The results include a table with all tested HPO terms
-ordered by the corrected p value (Benjamini-Hochberg FDR).
-Here we show the top 20 table rows:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.analysis.predicate</span> <span class="kn">import</span> <span class="n">PatientCategories</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">summarize</span><span class="p">(</span><span class="n">hpo</span><span class="p">,</span> <span class="n">PatientCategories</span><span class="o">.</span><span class="n">YES</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">20</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s1">&#39;docs/user-guide/report/tbx5_frameshift.csv&#39;</span><span class="p">)</span>  
+ordered by the corrected p value (Benjamini-Hochberg FDR):</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.view</span> <span class="kn">import</span> <span class="n">summarize_hpo_analysis</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span> <span class="o">=</span> <span class="n">summarize_hpo_analysis</span><span class="p">(</span><span class="n">hpo</span><span class="p">,</span> <span class="n">result</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">summary_df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s1">&#39;docs/user-guide/report/tbx5_frameshift.csv&#39;</span><span class="p">)</span>  
 </pre></div>
 </div>
 <table class="docutils align-default" id="id5">
 <caption><span class="caption-text"><em>TBX5</em> frameshift vs rest</span><a class="headerlink" href="#id5" title="Link to this table"></a></caption>
 <thead>
-<tr class="row-odd"><th class="head"><p>Which genotype group does the patient fit in: HOM_REF, HET</p></th>
+<tr class="row-odd"><th class="head"><p>What is the genotype group</p></th>
 <th class="head"><p>HOM_REF</p></th>
 <th class="head"><p>HOM_REF</p></th>
 <th class="head"><p>HET</p></th>
@@ -485,7 +448,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>59%</p></td>
 <td><p>19/19</p></td>
 <td><p>100%</p></td>
-<td><p>0.00411275392326226</p></td>
+<td><p>0.003870827221893892</p></td>
 <td><p>0.00024192670136836825</p></td>
 </tr>
 <tr class="row-even"><td><p>Abnormal atrioventricular conduction [HP:0005150]</p></td>
@@ -493,7 +456,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>4%</p></td>
 <td><p>3/3</p></td>
 <td><p>100%</p></td>
-<td><p>0.01307692307692308</p></td>
+<td><p>0.01230769230769231</p></td>
 <td><p>0.0015384615384615387</p></td>
 </tr>
 <tr class="row-odd"><td><p>Absent thumb [HP:0009777]</p></td>
@@ -501,7 +464,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>18%</p></td>
 <td><p>14/31</p></td>
 <td><p>45%</p></td>
-<td><p>0.021044138590779585</p></td>
+<td><p>0.01980624808543961</p></td>
 <td><p>0.003713671516019927</p></td>
 </tr>
 <tr class="row-even"><td><p>Atrioventricular block [HP:0001678]</p></td>
@@ -509,74 +472,66 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>4%</p></td>
 <td><p>2/2</p></td>
 <td><p>100%</p></td>
-<td><p>0.034</p></td>
+<td><p>0.04</p></td>
 <td><p>0.01</p></td>
 </tr>
-<tr class="row-odd"><td><p>Heart block [HP:0012722]</p></td>
-<td><p>1/23</p></td>
-<td><p>4%</p></td>
-<td><p>2/2</p></td>
-<td><p>100%</p></td>
-<td><p>0.034</p></td>
-<td><p>0.01</p></td>
-</tr>
-<tr class="row-even"><td><p>Patent ductus arteriosus [HP:0001643]</p></td>
+<tr class="row-odd"><td><p>Patent ductus arteriosus [HP:0001643]</p></td>
 <td><p>6/40</p></td>
 <td><p>15%</p></td>
 <td><p>2/2</p></td>
 <td><p>100%</p></td>
-<td><p>0.09214092140921408</p></td>
+<td><p>0.10406504065040649</p></td>
 <td><p>0.03252032520325203</p></td>
 </tr>
-<tr class="row-odd"><td><p>Secundum atrial septal defect [HP:0001684]</p></td>
+<tr class="row-even"><td><p>Secundum atrial septal defect [HP:0001684]</p></td>
 <td><p>23/55</p></td>
 <td><p>42%</p></td>
 <td><p>4/22</p></td>
 <td><p>18%</p></td>
-<td><p>0.1440020479198931</p></td>
+<td><p>0.15059037690969213</p></td>
 <td><p>0.06544319142266644</p></td>
 </tr>
-<tr class="row-even"><td><p>Triphalangeal thumb [HP:0001199]</p></td>
+<tr class="row-odd"><td><p>Triphalangeal thumb [HP:0001199]</p></td>
 <td><p>23/99</p></td>
 <td><p>23%</p></td>
 <td><p>13/32</p></td>
 <td><p>41%</p></td>
-<td><p>0.1440020479198931</p></td>
+<td><p>0.15059037690969213</p></td>
 <td><p>0.06932119159387057</p></td>
 </tr>
-<tr class="row-odd"><td><p>Cardiac conduction abnormality [HP:0031546]</p></td>
+<tr class="row-even"><td><p>Cardiac conduction abnormality [HP:0031546]</p></td>
 <td><p>15/37</p></td>
 <td><p>41%</p></td>
 <td><p>3/3</p></td>
 <td><p>100%</p></td>
-<td><p>0.1440020479198931</p></td>
+<td><p>0.15059037690969213</p></td>
 <td><p>0.08259109311740892</p></td>
 </tr>
-<tr class="row-even"><td><p>Muscular ventricular septal defect [HP:0011623]</p></td>
+<tr class="row-odd"><td><p>Muscular ventricular septal defect [HP:0011623]</p></td>
 <td><p>8/84</p></td>
 <td><p>10%</p></td>
 <td><p>6/25</p></td>
 <td><p>24%</p></td>
-<td><p>0.1440020479198931</p></td>
+<td><p>0.15059037690969213</p></td>
 <td><p>0.08470708701170182</p></td>
 </tr>
-<tr class="row-odd"><td><p>Pulmonary arterial hypertension [HP:0002092]</p></td>
+<tr class="row-even"><td><p>Pulmonary arterial hypertension [HP:0002092]</p></td>
 <td><p>8/14</p></td>
 <td><p>57%</p></td>
 <td><p>0/2</p></td>
 <td><p>0%</p></td>
-<td><p>0.6899307928951143</p></td>
+<td><p>0.708378140298727</p></td>
 <td><p>0.4666666666666667</p></td>
 </tr>
-<tr class="row-even"><td><p>Short thumb [HP:0009778]</p></td>
+<tr class="row-odd"><td><p>Short thumb [HP:0009778]</p></td>
 <td><p>25/69</p></td>
 <td><p>36%</p></td>
 <td><p>8/30</p></td>
 <td><p>27%</p></td>
-<td><p>0.6899307928951143</p></td>
+<td><p>0.708378140298727</p></td>
 <td><p>0.48700997145537483</p></td>
 </tr>
-<tr class="row-odd"><td><p>Absent radius [HP:0003974]</p></td>
+<tr class="row-even"><td><p>Absent radius [HP:0003974]</p></td>
 <td><p>9/43</p></td>
 <td><p>21%</p></td>
 <td><p>6/25</p></td>
@@ -584,7 +539,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>1.0</p></td>
 <td><p>0.7703831604944444</p></td>
 </tr>
-<tr class="row-even"><td><p>Atrial septal defect [HP:0001631]</p></td>
+<tr class="row-odd"><td><p>Atrial septal defect [HP:0001631]</p></td>
 <td><p>63/65</p></td>
 <td><p>97%</p></td>
 <td><p>20/20</p></td>
@@ -592,7 +547,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>1.0</p></td>
 <td><p>1.0</p></td>
 </tr>
-<tr class="row-odd"><td><p>Hypoplasia of the radius [HP:0002984]</p></td>
+<tr class="row-even"><td><p>Hypoplasia of the radius [HP:0002984]</p></td>
 <td><p>34/75</p></td>
 <td><p>45%</p></td>
 <td><p>6/14</p></td>
@@ -600,7 +555,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>1.0</p></td>
 <td><p>1.0</p></td>
 </tr>
-<tr class="row-even"><td><p>Hypoplasia of the ulna [HP:0003022]</p></td>
+<tr class="row-odd"><td><p>Hypoplasia of the ulna [HP:0003022]</p></td>
 <td><p>3/17</p></td>
 <td><p>18%</p></td>
 <td><p>2/10</p></td>
@@ -608,7 +563,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>1.0</p></td>
 <td><p>1.0</p></td>
 </tr>
-<tr class="row-odd"><td><p>Short humerus [HP:0005792]</p></td>
+<tr class="row-even"><td><p>Short humerus [HP:0005792]</p></td>
 <td><p>8/21</p></td>
 <td><p>38%</p></td>
 <td><p>4/9</p></td>
@@ -616,30 +571,6 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 <td><p>1.0</p></td>
 <td><p>1.0</p></td>
 </tr>
-<tr class="row-even"><td><p>Abnormal atrial septum morphology [HP:0011994]</p></td>
-<td><p>64/64</p></td>
-<td><p>100%</p></td>
-<td><p>20/20</p></td>
-<td><p>100%</p></td>
-<td></td>
-<td></td>
-</tr>
-<tr class="row-odd"><td><p>Abnormal cardiac septum morphology [HP:0001671]</p></td>
-<td><p>89/89</p></td>
-<td><p>100%</p></td>
-<td><p>28/28</p></td>
-<td><p>100%</p></td>
-<td></td>
-<td></td>
-</tr>
-<tr class="row-even"><td><p>Abnormal heart morphology [HP:0001627]</p></td>
-<td><p>89/89</p></td>
-<td><p>100%</p></td>
-<td><p>30/30</p></td>
-<td><p>100%</p></td>
-<td></td>
-<td></td>
-</tr>
 </tbody>
 </table>
 <p>The table shows that several HPO terms are significantly associated
@@ -649,7 +580,7 @@ <h5>Genotype phenotype associations<a class="headerlink" href="#genotype-phenoty
 but it was observed in 19/19 (100%) patients with a frameshift variant.
 Fisher exact test computed a p value of <cite>~0.000242</cite>
 and the p value corrected by Benjamini-Hochberg procedure
-is <cite>~0.00411</cite>.</p>
+is <cite>~0.00387</cite>.</p>
 <p>The table includes all HPO terms of the cohort, including the terms that were not selected for testing
 and thus have no associated p value.</p>
 </section>
@@ -707,7 +638,7 @@ <h4>Example<a class="headerlink" href="#id2" title="Link to this heading"></a
 <p>which we will use to preprocess the cohort</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">gpsea.preprocessing</span> <span class="kn">import</span> <span class="n">load_phenopackets</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">cohort</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">load_phenopackets</span><span class="p">(</span><span class="n">phenopackets</span><span class="p">,</span> <span class="n">cohort_creator</span><span class="p">)</span>  
-<span class="go">Patients Created: ...</span>
+<span class="go">Individuals Processed: ...</span>
 </pre></div>
 </div>
 <p>resulting in a cohort consisting of 19 individuals</p>
@@ -894,7 +825,7 @@ <h5>Analysis<a class="headerlink" href="#id4" title="Link to this heading"></
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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