update documentation

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: cc58d845cfaa992b2416162d1b1281e5
+config: 55b60ac254bb232864915e417b1f8d37
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/installation/index.rst.txt

@@ -14,10 +14,10 @@ Docker image
 
 ::
 
-    docker pull kenjikamimoto126/celloracle_ubuntu:0.12.0
+    docker pull kenjikamimoto126/celloracle_ubuntu:0.18.0
 
 
-- This docker image was built based on Ubuntu 20.04.
+- This docker image was built based on Ubuntu 20.04 and python 3.10.
 - Python dependent packages and celloracle are installed in an anaconda environment, celloracle_env. This environment will be activated automatically when you log in.
 
 .. toctree::

_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.17.1',
+    VERSION: '0.18.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

changelog/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Changelog &mdash; celloracle 0.17.1 documentation</title>
+  <title>Changelog &mdash; celloracle 0.18.0 documentation</title>
 
 
 

citation/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Authors and citations &mdash; celloracle 0.17.1 documentation</title>
+  <title>Authors and citations &mdash; celloracle 0.18.0 documentation</title>
 
 
 

contact/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Contact &mdash; celloracle 0.17.1 documentation</title>
+  <title>Contact &mdash; celloracle 0.18.0 documentation</title>
 
 
 

genindex.html

@@ -18,7 +18,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Index &mdash; celloracle 0.17.1 documentation</title>
+  <title>Index &mdash; celloracle 0.18.0 documentation</title>
 
 
 

google_colab/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Google Colaboratoly &mdash; celloracle 0.17.1 documentation</title>
+  <title>Google Colaboratoly &mdash; celloracle 0.18.0 documentation</title>
 
 
 

index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Welcome to CellOracle’s documentation! &mdash; celloracle 0.17.1 documentation</title>
+  <title>Welcome to CellOracle’s documentation! &mdash; celloracle 0.18.0 documentation</title>
 
 
 

installation/R_step_by_step_installation.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>R dependent library installation troubleshooting &mdash; celloracle 0.17.1 documentation</title>
+  <title>R dependent library installation troubleshooting &mdash; celloracle 0.18.0 documentation</title>
 
 
 

installation/check_installation.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Check python library installation status &mdash; celloracle 0.17.1 documentation</title>
+  <title>Check python library installation status &mdash; celloracle 0.18.0 documentation</title>
 
 
 

installation/docker_additional_information.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>CellOracle docker image quick start and additional notes &mdash; celloracle 0.17.1 documentation</title>
+  <title>CellOracle docker image quick start and additional notes &mdash; celloracle 0.18.0 documentation</title>
 
 
 

installation/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Installation &mdash; celloracle 0.17.1 documentation</title>
+  <title>Installation &mdash; celloracle 0.18.0 documentation</title>
 
 
 
@@ -234,11 +234,11 @@
 <ul class="simple">
 <li><p>Pre-built docker image is available through <a class="reference external" href="https://hub.docker.com/repository/docker/kenjikamimoto126/celloracle_ubuntu">Docker Hub</a> .</p></li>
 </ul>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">pull</span> <span class="n">kenjikamimoto126</span><span class="o">/</span><span class="n">celloracle_ubuntu</span><span class="p">:</span><span class="mf">0.12</span><span class="o">.</span><span class="mi">0</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">pull</span> <span class="n">kenjikamimoto126</span><span class="o">/</span><span class="n">celloracle_ubuntu</span><span class="p">:</span><span class="mf">0.18</span><span class="o">.</span><span class="mi">0</span>
 </pre></div>
 </div>
 <ul class="simple">
-<li><p>This docker image was built based on Ubuntu 20.04.</p></li>
+<li><p>This docker image was built based on Ubuntu 20.04 and python 3.10.</p></li>
 <li><p>Python dependent packages and celloracle are installed in an anaconda environment, celloracle_env. This environment will be activated automatically when you log in.</p></li>
 </ul>
 <div class="toctree-wrapper compound">

installation/python_step_by_step_installation.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Python dependent library installation troubleshooting &mdash; celloracle 0.17.1 documentation</title>
+  <title>Python dependent library installation troubleshooting &mdash; celloracle 0.18.0 documentation</title>
 
 
 

license/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>License &mdash; celloracle 0.17.1 documentation</title>
+  <title>License &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.data.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.data module &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.data module &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.data_conversion.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.data_conversion module &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.data_conversion module &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.go_analysis.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.go_analysis module &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.go_analysis module &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Custom class in celloracle &mdash; celloracle 0.17.1 documentation</title>
+  <title>Custom class in celloracle &mdash; celloracle 0.18.0 documentation</title>
 
 
 
@@ -370,7 +370,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>gois</strong> (<em>list of srt</em>) – List of gene name to highlight.</p></li>
 <li><p><strong>clusters</strong> (<em>list of str</em>) – List of cluster name to analyze. If None, all clusters in Links object will be analyzed.</p></li>
 <li><p><strong>scatter</strong> (<em>bool</em>) – Whether to make a scatter plot.</p></li>
@@ -395,7 +395,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>gois</strong> (<em>list of srt</em>) – List of gene name to highlight.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.</p></li>
@@ -412,7 +412,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>plot_model</strong> (<em>bool</em>) – Whether to plot linear approximation line.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.</p></li>
@@ -446,7 +446,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>value</strong> (<em>srt</em>) – The network score type.</p></li>
 <li><p><strong>cluster1</strong> (<em>str</em>) – Cluster name. Network scores in cluster1 will be visualized in the x-axis.</p></li>
 <li><p><strong>cluster2</strong> (<em>str</em>) – Cluster name. Network scores in cluster2 will be visualized in the y-axis.</p></li>
@@ -467,7 +467,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See Links class for details.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See Links class for details.</p></li>
 <li><p><strong>values</strong> (<em>list of str</em>) – The list of score to visualize. If it is None, all of the network score will be used.</p></li>
 <li><p><strong>method</strong> (<em>str</em>) – Plotting method. Select either “boxplot” or “barplot”.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
@@ -485,7 +485,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>goi</strong> (<em>srt</em>) – Gene name.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.</p></li>
@@ -501,7 +501,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>cluster</strong> (<em>str</em>) – Cluster name to analyze.</p></li>
 <li><p><strong>n_gene</strong> (<em>int</em>) – Number of genes to plot. Default is 50.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
@@ -1068,7 +1068,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 This function can be used to reconstruct GRNs based on pre-existing GRNs saved in Links object.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>links_object</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – Please see the explanation of Links class.</p>
+<dd class="field-odd"><p><strong>links_object</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – Please see the explanation of Links class.</p>
 </dd>
 </dl>
 </dd></dl>

modules/celloracle.motif_analysis.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.motif_analysis module &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.motif_analysis module &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.network.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.network package &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.network package &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.network_analysis.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.network_analysis module &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.network_analysis module &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/celloracle.utility.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>celloracle.utility module &mdash; celloracle 0.17.1 documentation</title>
+  <title>celloracle.utility module &mdash; celloracle 0.18.0 documentation</title>
 
 
 

modules/index.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>API &mdash; celloracle 0.17.1 documentation</title>
+  <title>API &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/01_atacdata_analysis_with_cicero_and_monocle3.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; celloracle 0.17.1 documentation</title>
+  <title>Overview &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/02_preprocess_peak_data.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; celloracle 0.17.1 documentation</title>
+  <title>Overview &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/1_make_tss_referenece_from_ensemble_gff3_file.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; celloracle 0.17.1 documentation</title>
+  <title>Overview &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/tss_annotation_using_custom_tss_data.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; celloracle 0.17.1 documentation</title>
+  <title>Overview &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Xenbase database/1_make_tss_referenece_from_Xenbase_gff3_file.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; celloracle 0.17.1 documentation</title>
+  <title>Overview &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-Arabidopsis.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>1. Download and unzip annotation data &mdash; celloracle 0.17.1 documentation</title>
+  <title>1. Download and unzip annotation data &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-other_species.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>1. Download and unzip annotation data &mdash; celloracle 0.17.1 documentation</title>
+  <title>1. Download and unzip annotation data &mdash; celloracle 0.18.0 documentation</title>
 
 
 

notebooks/01_ATAC-seq_data_processing/option2_Bulk_ATAC-seq_data/01_preprocess_Bulk_ATAC_seq_peak_data.html

@@ -19,7 +19,7 @@
     </script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; celloracle 0.17.1 documentation</title>
+  <title>Overview &mdash; celloracle 0.18.0 documentation</title>