From 88c988fc1434586c1502895c101f76ba6476eac3 Mon Sep 17 00:00:00 2001 From: ielis Date: Thu, 21 Nov 2024 20:53:26 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20monarch-?= =?UTF-8?q?initiative/gpsea@218e35b1d3a098d74cdb75146df4a61bf3a7d7e4=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- latest/_modules/gpsea/analysis/_base.html | 106 ++++++++++++++---- .../_modules/gpsea/analysis/pcats/_impl.html | 39 +++---- .../gpsea/analysis/pcats/stats/_stats.html | 28 +++-- .../_modules/gpsea/analysis/pscore/_api.html | 12 +- .../gpsea/analysis/pscore/stats/_stats.html | 36 +++--- .../gpsea/analysis/temporal/_api.html | 12 +- .../gpsea/analysis/temporal/stats/_api.html | 4 +- .../gpsea/analysis/temporal/stats/_impl.html | 8 +- latest/apidocs/gpsea.analysis.html | 52 ++++++++- latest/apidocs/gpsea.analysis.pcats.html | 11 +- .../apidocs/gpsea.analysis.pcats.stats.html | 6 +- latest/apidocs/gpsea.analysis.pscore.html | 2 +- .../apidocs/gpsea.analysis.pscore.stats.html | 15 ++- latest/apidocs/gpsea.analysis.temporal.html | 2 +- .../gpsea.analysis.temporal.stats.html | 6 +- latest/apidocs/gpsea.html | 2 + latest/genindex.html | 30 ++++- latest/objects.inv | Bin 8144 -> 8201 bytes latest/searchindex.js | 2 +- 19 files changed, 272 insertions(+), 101 deletions(-) diff --git a/latest/_modules/gpsea/analysis/_base.html b/latest/_modules/gpsea/analysis/_base.html index 2fcac770..d45a9dbb 100644 --- a/latest/_modules/gpsea/analysis/_base.html +++ b/latest/_modules/gpsea/analysis/_base.html @@ -93,6 +93,61 @@

Source code for gpsea.analysis._base

 from ._partition import Partitioning
 
 
+

+[docs]
+class StatisticResult:
+    """
+    `StatisticResult` reports result of a :class:`~gpsea.analysis.Statistic`.
+
+    It includes a statistic and a corresponding p value.
+    """
+
+    def __init__(
+        self,
+        statistic: typing.Optional[typing.Union[int, float]],
+        pval: float,
+    ):
+        if statistic is not None:
+            assert isinstance(statistic, (float, int))
+            self._statistic = float(statistic)
+        else:
+            self._statistic = None
+
+        if isinstance(pval, float) and (math.isnan(pval) or 0.0 <= pval <= 1.0):
+            self._pval = float(pval)
+        else:
+            raise ValueError(
+                f"`pval` must be a float in range [0, 1] but it was {pval}"
+            )
+
+    @property
+    def statistic(self) -> typing.Optional[float]:
+        return self._statistic
+
+    @property
+    def pval(self) -> float:
+        return self._pval
+
+    def __eq__(self, value: object) -> bool:
+        return (
+            isinstance(value, StatisticResult)
+            and self._statistic == value._statistic
+            and self._pval == value._pval
+        )
+
+    def __hash__(self) -> int:
+        return hash((self._statistic, self._pval,))
+
+    def __str__(self) -> str:
+        return repr(self)
+
+    def __repr__(self) -> str:
+        return f"StatisticResult(statistic={self._statistic}, pval={self._pval})"

+
+
+
+

+[docs]
 class Statistic(metaclass=abc.ABCMeta):
     """
     Mixin for classes that are used to compute a nominal p value for a genotype-phenotype association.
@@ -117,7 +172,8 @@ 
Source code for gpsea.analysis._base
         return NotImplemented
     
     def __hash__(self) -> int:
-        return hash((self._name,))
+        return hash((self._name,))

+
 
 
 

@@ -180,7 +236,7 @@ 
Source code for gpsea.analysis._base
         statistic: Statistic,
         n_usable: typing.Sequence[int],
         all_counts: typing.Sequence[pd.DataFrame],
-        pvals: typing.Sequence[float],
+        statistic_results: typing.Sequence[typing.Optional[StatisticResult]],
         corrected_pvals: typing.Optional[typing.Sequence[float]],
         mtc_correction: typing.Optional[str]
     ):
@@ -194,7 +250,7 @@ 
Source code for gpsea.analysis._base
         self._n_usable = tuple(n_usable)
         self._all_counts = tuple(all_counts)
 
-        self._pvals = tuple(pvals)
+        self._statistic_results = tuple(statistic_results)
         self._corrected_pvals = (
             None if corrected_pvals is None else tuple(corrected_pvals)
         )
@@ -212,7 +268,7 @@ 
Source code for gpsea.analysis._base
         for seq, name in (
             (self._n_usable, 'n_usable'),
             (self._all_counts, 'all_counts'),
-            (self._pvals, 'pvals'),
+            (self._statistic_results, 'statistic_results'),
         ):
             if len(self._pheno_predicates) != len(seq):
                 errors.append(
@@ -277,13 +333,21 @@ 
Source code for gpsea.analysis._base
         """
         return self._all_counts
 
+    @property
+    def statistic_results(self) -> typing.Sequence[typing.Optional[StatisticResult]]:
+        """
+        Get a sequence of :class:`~gpsea.analysis.StatisticResult` items with nominal p values and the associated statistic values
+        for each tested phenotype or `None` for the untested phenotypes.
+        """
+        return self._statistic_results
+
     @property
     def pvals(self) -> typing.Sequence[float]:
         """
         Get a sequence of nominal p values for each tested phenotype.
         The sequence includes a `NaN` value for each phenotype that was *not* tested.
         """
-        return self._pvals
+        return tuple(float('nan') if r is None else r.pval for r in self._statistic_results )
 
     @property
     def corrected_pvals(self) -> typing.Optional[typing.Sequence[float]]:
@@ -341,13 +405,12 @@ 
Source code for gpsea.analysis._base
         return tuple(int(idx) for idx in np.argsort(vals) if selected[idx])

 
 
-
     @property
     def total_tests(self) -> int:
         """
         Get total count of genotype-phenotype associations that were tested in this analysis.
         """
-        return sum(1 for pval in self.pvals if not math.isnan(pval))
+        return sum(1 for result in self._statistic_results if result is not None)
 
     @property
     def mtc_correction(self) -> typing.Optional[str]:
@@ -363,7 +426,7 @@ 
Source code for gpsea.analysis._base
             and self._pheno_predicates == value._pheno_predicates \
             and self._n_usable == value._n_usable \
             and self._all_counts == value._all_counts \
-            and self._pvals == value._pvals \
+            and self._statistic_results == value._statistic_results \
             and self._corrected_pvals == value._corrected_pvals \
             and self._mtc_correction == value._mtc_correction
     
@@ -373,7 +436,7 @@ 
Source code for gpsea.analysis._base
             self._pheno_predicates,
             self._n_usable,
             self._all_counts,
-            self._pvals,
+            self._statistic_results,
             self._corrected_pvals,
             self._mtc_correction,
         ))

@@ -409,7 +472,7 @@ 
Source code for gpsea.analysis._base
         phenotype: Partitioning,
         statistic: Statistic,
         data: pd.DataFrame,
-        pval: float,
+        statistic_result: StatisticResult,
     ):
         super().__init__(gt_predicate, statistic)
 
@@ -421,12 +484,8 @@ 
Source code for gpsea.analysis._base
         )
         self._data = data
 
-        if isinstance(pval, float) and math.isfinite(pval) and 0.0 <= pval <= 1.0:
-            self._pval = float(pval)
-        else:
-            raise ValueError(
-                f"`pval` must be a finite float in range [0, 1] but it was {pval}"
-            )
+        assert isinstance(statistic_result, StatisticResult)
+        self._statistic_result = statistic_result
         
     @property
     def phenotype(self) -> Partitioning:
@@ -469,25 +528,34 @@ 
Source code for gpsea.analysis._base
         ]

 
 
+

+[docs]
+    def statistic_result(self) -> StatisticResult:
+        """
+        Get statistic result with the nominal p value and the associated statistics.
+        """
+        return self._statistic_result

+
+
     @property
     def pval(self) -> float:
         """
         Get the p value of the test.
         """
-        return self._pval
+        return self._statistic_result.pval
 
     def __eq__(self, value: object) -> bool:
         return isinstance(value, MonoPhenotypeAnalysisResult) \
             and super(AnalysisResult, self).__eq__(value) \
             and self._phenotype == value._phenotype \
-            and self._pval == value._pval \
+            and self._statistic_result == value._statistic_result \
             and self._data.equals(value._data)
     
     def __hash__(self) -> int:
         return hash((
             super(AnalysisResult, self).__hash__(),
             self._phenotype,
-            self._pval,
+            self._statistic_result,
             self._data,
         ))

 
diff --git a/latest/_modules/gpsea/analysis/pcats/_impl.html b/latest/_modules/gpsea/analysis/pcats/_impl.html
index 5da0049f..f18d9bd2 100644
--- a/latest/_modules/gpsea/analysis/pcats/_impl.html
+++ b/latest/_modules/gpsea/analysis/pcats/_impl.html
@@ -99,7 +99,7 @@ 
Source code for gpsea.analysis.pcats._impl
 from ..mtc_filter import PhenotypeMtcFilter, PhenotypeMtcResult
 
 from .stats import CountStatistic
-from .._base import MultiPhenotypeAnalysisResult
+from .._base import MultiPhenotypeAnalysisResult, StatisticResult
 
 DEFAULT_MTC_PROCEDURE = 'fdr_bh'
 """
@@ -283,30 +283,31 @@ 
Source code for gpsea.analysis.pcats._impl
 
         return issues
 
-    def _compute_nominal_pvals(
+    def _compute_nominal_stats(
         self,
         n_usable: typing.Iterable[int],
         all_counts: typing.Iterable[pd.DataFrame],
-    ) -> np.ndarray:
-        pvals = []
+    ) -> typing.Sequence[typing.Optional[StatisticResult]]:
+        results = []
         for i, (usable, count) in enumerate(zip(n_usable, all_counts)):
             if usable == 0:
-                pvals.append(np.nan)
+                results.append(None)
             else:
                 try:
-                    pval = self._count_statistic.compute_pval(count)
-                    pvals.append(pval)
+                    stat_result = self._count_statistic.compute_pval(count)
+                    results.append(stat_result)
                 except ValueError as ve:
                     # TODO: add more context to the exception?
                     raise ve
 
-        return np.array(pvals)
+        return np.array(results)
 
     def _apply_mtc(
         self,
-        pvals: typing.Sequence[float],
+        stats: typing.Sequence[typing.Optional[StatisticResult]],
     ) -> typing.Sequence[float]:
         assert self._mtc_correction is not None
+        pvals = tuple(s.pval for s in stats if s is not None)
         _, corrected_pvals, _, _ = multitest.multipletests(
             pvals=pvals,
             alpha=self._mtc_alpha,
@@ -340,13 +341,13 @@ 
Source code for gpsea.analysis.pcats._impl
         )
 
         # 2 - Compute nominal p values
-        pvals = self._compute_nominal_pvals(n_usable=n_usable, all_counts=all_counts)
+        stats = self._compute_nominal_stats(n_usable=n_usable, all_counts=all_counts)
 
         # 3 - Apply Multiple Testing Correction
         if self._mtc_correction is None:
             corrected_pvals = None
         else:
-            corrected_pvals = self._apply_mtc(pvals=pvals)
+            corrected_pvals = self._apply_mtc(stats=stats)
 
         return MultiPhenotypeAnalysisResult(
             gt_predicate=gt_predicate,
@@ -355,7 +356,7 @@ 
Source code for gpsea.analysis.pcats._impl
             pheno_predicates=pheno_predicates,
             n_usable=n_usable,
             all_counts=all_counts,
-            pvals=pvals,
+            statistic_results=stats,
             corrected_pvals=corrected_pvals,
         )

 
@@ -379,7 +380,7 @@ 
Source code for gpsea.analysis.pcats._impl
         pheno_predicates: typing.Iterable[PhenotypePolyPredicate[hpotk.TermId]],
         n_usable: typing.Sequence[int],
         all_counts: typing.Sequence[pd.DataFrame],
-        pvals: typing.Sequence[float],
+        statistic_results: typing.Sequence[typing.Optional[StatisticResult]],
         corrected_pvals: typing.Optional[typing.Sequence[float]],
         mtc_filter_name: str,
         mtc_filter_results: typing.Sequence[PhenotypeMtcResult],
@@ -391,7 +392,7 @@ 
Source code for gpsea.analysis.pcats._impl
             statistic=statistic,
             n_usable=n_usable,
             all_counts=all_counts,
-            pvals=pvals,
+            statistic_results=statistic_results,
             corrected_pvals=corrected_pvals,
             mtc_correction=mtc_correction,
         )
@@ -503,7 +504,7 @@ 
Source code for gpsea.analysis.pcats._impl
             cohort_size=cohort_size,
         )
 
-        pvals = np.full(shape=(len(n_usable),), fill_value=np.nan)
+        results = np.full(shape=(len(n_usable),), fill_value=None)
         corrected_pvals = None
 
         mtc_mask = np.array([r.is_passed() for r in mtc_filter_results])
@@ -511,16 +512,16 @@ 
Source code for gpsea.analysis.pcats._impl
             # We have at least one HPO term to test.
 
             # 3 - Compute nominal p values
-            pvals[mtc_mask] = self._compute_nominal_pvals(
+            results[mtc_mask] = self._compute_nominal_stats(
                 n_usable=slice_list_in_numpy_style(n_usable, mtc_mask),
                 all_counts=slice_list_in_numpy_style(all_counts, mtc_mask),
             )
 
             # 4 - Apply Multiple Testing Correction
             if self._mtc_correction is not None:
-                corrected_pvals = np.full(shape=pvals.shape, fill_value=np.nan)
+                corrected_pvals = np.full(shape=results.shape, fill_value=np.nan)
                 # Do not test the p values that have been filtered out.
-                corrected_pvals[mtc_mask] = self._apply_mtc(pvals=pvals[mtc_mask])
+                corrected_pvals[mtc_mask] = self._apply_mtc(stats=results[mtc_mask])
 
         return HpoTermAnalysisResult(
             gt_predicate=gt_predicate,
@@ -529,7 +530,7 @@ 
Source code for gpsea.analysis.pcats._impl
             pheno_predicates=pheno_predicates,
             n_usable=n_usable,
             all_counts=all_counts,
-            pvals=pvals,
+            statistic_results=results,
             corrected_pvals=corrected_pvals,
             mtc_filter_name=self._mtc_filter.filter_method_name(),
             mtc_filter_results=mtc_filter_results,
diff --git a/latest/_modules/gpsea/analysis/pcats/stats/_stats.html b/latest/_modules/gpsea/analysis/pcats/stats/_stats.html
index 864afde4..5a9a0265 100644
--- a/latest/_modules/gpsea/analysis/pcats/stats/_stats.html
+++ b/latest/_modules/gpsea/analysis/pcats/stats/_stats.html
@@ -90,9 +90,9 @@ 
Source code for gpsea.analysis.pcats.stats._stats
import numpy as np
 import pandas as pd
 
-import scipy
+from scipy.stats import fisher_exact
 
-from ..._base import Statistic
+from ..._base import Statistic, StatisticResult
 
 
 

@@ -150,7 +150,7 @@ 
Source code for gpsea.analysis.pcats.stats._stats
def compute_pval(
         self,
         counts: pd.DataFrame,
-    ) -> float:
+    ) -> StatisticResult:
         pass

 
 
@@ -190,12 +190,19 @@ 
Source code for gpsea.analysis.pcats.stats._stats
def compute_pval(
         self,
         counts: pd.DataFrame,
-    ) -> float:
+    ) -> StatisticResult:
         if counts.shape == (2, 2):
-            _, pval = scipy.stats.fisher_exact(counts.values, alternative="two-sided")
-            return pval
+            result = fisher_exact(counts.values, alternative="two-sided")
+            return StatisticResult(
+                statistic=result.statistic,
+                pval=result.pvalue,
+            )
         elif counts.shape == (2, 3):
-            return self._fisher_exact(counts.values)
+            pval = self._fisher_exact(counts.values)
+            return StatisticResult(
+                statistic=None,
+                pval=pval,
+            )
         else:
             raise ValueError(f'Unsupported counts shape {counts.shape}')

 
@@ -239,11 +246,12 @@ 
Source code for gpsea.analysis.pcats.stats._stats
p_0 /= Decimal(math.factorial(table[i][j]))
 
         p = [0]
-        self._dfs(mat, pos, row_sum, col_sum, p_0, p)
+        FisherExactTest._dfs(mat, pos, row_sum, col_sum, p_0, p)
 
         return float(p[0])
 
-    def _dfs(self, mat, pos, r_sum, c_sum, p_0, p):
+    @staticmethod
+    def _dfs(mat, pos, r_sum, c_sum, p_0, p):
 
         (xx, yy) = pos
         (r, c) = (len(r_sum), len(c_sum))
@@ -307,7 +315,7 @@ 
Source code for gpsea.analysis.pcats.stats._stats
pos_new = (0, yy + 1)
                 else:
                     pos_new = (xx + 1, yy)
-                self._dfs(mat_new, pos_new, r_sum, c_sum, p_0, p)
+                FisherExactTest._dfs(mat_new, pos_new, r_sum, c_sum, p_0, p)
 
     def __eq__(self, value: object) -> bool:
         return isinstance(value, FisherExactTest)
diff --git a/latest/_modules/gpsea/analysis/pscore/_api.html b/latest/_modules/gpsea/analysis/pscore/_api.html
index be870f46..944f6a88 100644
--- a/latest/_modules/gpsea/analysis/pscore/_api.html
+++ b/latest/_modules/gpsea/analysis/pscore/_api.html
@@ -89,7 +89,7 @@ 
Source code for gpsea.analysis.pscore._api
 from ..predicate.genotype import GenotypePolyPredicate
 from .stats import PhenotypeScoreStatistic
 
-from .._base import MonoPhenotypeAnalysisResult, Statistic
+from .._base import MonoPhenotypeAnalysisResult, Statistic, StatisticResult
 from .._partition import ContinuousPartitioning
 
 
@@ -215,9 +215,9 @@ 
Source code for gpsea.analysis.pscore._api
         phenotype: PhenotypeScorer,
         statistic: Statistic,
         data: pd.DataFrame,
-        pval: float,
+        statistic_result: StatisticResult,
     ):
-        super().__init__(gt_predicate, phenotype, statistic, data, pval)
+        super().__init__(gt_predicate, phenotype, statistic, data, statistic_result)
         assert isinstance(phenotype, PhenotypeScorer)
 
 

@@ -291,7 +291,7 @@ 
Source code for gpsea.analysis.pscore._api
             f"phenotype_scorer={self._phenotype}, "
             f"statistic={self._statistic}, "
             f"data={self._data}, "
-            f"pval={self._pval})"
+            f"statistic_result={self._statistic_result})"
         )
 
     def __repr__(self) -> str:
@@ -366,14 +366,14 @@ 
Source code for gpsea.analysis.pscore._api
         y = data.loc[
             data[MonoPhenotypeAnalysisResult.GT_COL] == y_key, MonoPhenotypeAnalysisResult.PH_COL
         ].to_numpy(dtype=float)  # type: ignore
-        pval = self._statistic.compute_pval(scores=(x, y))
+        result = self._statistic.compute_pval(scores=(x, y))
 
         return PhenotypeScoreAnalysisResult(
             gt_predicate=gt_predicate,
             phenotype=pheno_scorer,
             statistic=self._statistic,
             data=data,
-            pval=pval,
+            statistic_result=result,
         )

 

 
diff --git a/latest/_modules/gpsea/analysis/pscore/stats/_stats.html b/latest/_modules/gpsea/analysis/pscore/stats/_stats.html
index 2f5d1aa6..f5da41d5 100644
--- a/latest/_modules/gpsea/analysis/pscore/stats/_stats.html
+++ b/latest/_modules/gpsea/analysis/pscore/stats/_stats.html
@@ -86,7 +86,7 @@ 
Source code for gpsea.analysis.pscore.stats._stats
from scipy.stats import mannwhitneyu, ttest_ind
 
-from ..._base import Statistic
+from ..._base import Statistic, StatisticResult
 
 
 

@@ -104,13 +104,13 @@ 
Source code for gpsea.analysis.pscore.stats._stats
def compute_pval(
         self,
         scores: typing.Collection[typing.Sequence[float]],
-    ) -> float:
+    ) -> StatisticResult:
         pass

 
 
     def __eq__(self, value: object) -> bool:
         return super().__eq__(value)
-    
+
     def __hash__(self) -> int:
         return super().__hash__()

 
@@ -128,7 +128,7 @@ 
Source code for gpsea.analysis.pscore.stats._stats
    See :ref:`phenotype-score-stats` for an example usage.
     """
-    
+
     def __init__(self):
         super().__init__(
             name="Mann-Whitney U test",
@@ -139,19 +139,22 @@ 
Source code for gpsea.analysis.pscore.stats._stats
def compute_pval(
         self,
         scores: typing.Collection[typing.Sequence[float]],
-    ) -> float:
+    ) -> StatisticResult:
         assert len(scores) == 2, 'Mann-Whitney U rank test only supports 2 categories at this time'
-        
+
         x, y = scores
         x = MannWhitneyStatistic._remove_nans(x)
         y = MannWhitneyStatistic._remove_nans(y)
-        _, pval = mannwhitneyu(
+        statistic, pval = mannwhitneyu(
             x=x,
             y=y,
             alternative='two-sided',
         )
 
-        return pval

+        return StatisticResult(
+            statistic=float(statistic),
+            pval=float(pval),
+        )

 
 
     @staticmethod
@@ -162,7 +165,7 @@ 
Source code for gpsea.analysis.pscore.stats._stats
def __eq__(self, value: object) -> bool:
         return isinstance(value, MannWhitneyStatistic)
-    
+
     def __hash__(self) -> int:
         return 23

 
@@ -191,9 +194,13 @@ 
Source code for gpsea.analysis.pscore.stats._stats
def compute_pval(
         self,
         scores: typing.Collection[typing.Sequence[float]],
-    ) -> float:
+    ) -> StatisticResult:
+        """
+        :Returns:
+            a tuple with the p-value and the t-statistic
+        """
         assert len(scores) == 2, 'T test only supports 2 categories at this time'
-        
+
         x, y = scores
         res = ttest_ind(
             a=x, b=y,
@@ -201,12 +208,15 @@ 
Source code for gpsea.analysis.pscore.stats._stats
nan_policy="omit",
         )
 
-        return res.pvalue

+        return StatisticResult(
+            statistic=float(res.statistic),
+            pval=float(res.pvalue),
+        )

 
 
     def __eq__(self, value: object) -> bool:
         return isinstance(value, TTestStatistic)
-    
+
     def __hash__(self) -> int:
         return 31

 
diff --git a/latest/_modules/gpsea/analysis/temporal/_api.html b/latest/_modules/gpsea/analysis/temporal/_api.html
index e033787d..ef78fd0d 100644
--- a/latest/_modules/gpsea/analysis/temporal/_api.html
+++ b/latest/_modules/gpsea/analysis/temporal/_api.html
@@ -95,7 +95,7 @@ 
Source code for gpsea.analysis.temporal._api
from ._util import prepare_censored_data
 from .stats import SurvivalStatistic
 
-from .._base import MonoPhenotypeAnalysisResult
+from .._base import MonoPhenotypeAnalysisResult, StatisticResult
 from .._partition import ContinuousPartitioning
 
 
@@ -159,14 +159,14 @@ 
Source code for gpsea.analysis.temporal._api
endpoint: Endpoint,
         statistic: SurvivalStatistic,
         data: pd.DataFrame,
-        pval: float,
+        statistic_result: StatisticResult,
     ):
         super().__init__(
             gt_predicate=gt_predicate,
             phenotype=endpoint,
             statistic=statistic,
             data=data,
-            pval=pval,
+            statistic_result=statistic_result,
         )
         assert isinstance(endpoint, Endpoint)
 
@@ -224,7 +224,7 @@ 
Source code for gpsea.analysis.temporal._api
f"endpoint={self._phenotype}, "
             f"statistic={self._statistic}, "
             f"data={self._data}, "
-            f"pval={self._pval})"
+            f"statistic_result={self._statistic_result})"
         )
 
     def __repr__(self) -> str:
@@ -285,14 +285,14 @@ 
Source code for gpsea.analysis.temporal._api
survivals[gt_cat].append(survival)
 
         vals = tuple(survivals[gt_cat] for gt_cat in gt_predicate.get_categorizations())
-        pval = self._statistic.compute_pval(vals)
+        result = self._statistic.compute_pval(vals)
 
         return SurvivalAnalysisResult(
             gt_predicate=gt_predicate,
             endpoint=endpoint,
             statistic=self._statistic,
             data=data,
-            pval=pval,
+            statistic_result=result,
         )

 

 
diff --git a/latest/_modules/gpsea/analysis/temporal/stats/_api.html b/latest/_modules/gpsea/analysis/temporal/stats/_api.html
index 4ecf9de5..326b6b04 100644
--- a/latest/_modules/gpsea/analysis/temporal/stats/_api.html
+++ b/latest/_modules/gpsea/analysis/temporal/stats/_api.html
@@ -83,7 +83,7 @@ 
Source code for gpsea.analysis.temporal.stats._api
import abc
 import typing
 
-from ..._base import Statistic
+from ..._base import Statistic, StatisticResult
 from .._base import Survival
 
 
@@ -105,7 +105,7 @@ 
Source code for gpsea.analysis.temporal.stats._api
def compute_pval(
         self,
         scores: typing.Collection[typing.Sequence[Survival]],
-    ) -> float:
+    ) -> StatisticResult:
         """
         Compute p value for the collection of survivals being sampled from
         the same source distribution.
diff --git a/latest/_modules/gpsea/analysis/temporal/stats/_impl.html b/latest/_modules/gpsea/analysis/temporal/stats/_impl.html
index 08226522..71fcb0d2 100644
--- a/latest/_modules/gpsea/analysis/temporal/stats/_impl.html
+++ b/latest/_modules/gpsea/analysis/temporal/stats/_impl.html
@@ -84,6 +84,7 @@ 
Source code for gpsea.analysis.temporal.stats._impl
from scipy import stats
 
+from ..._base import StatisticResult
 from .._base import Survival
 from .._util import prepare_censored_data
 from ._api import SurvivalStatistic
@@ -109,7 +110,7 @@ 
Source code for gpsea.analysis.temporal.stats._impl
def compute_pval(
         self,
         scores: typing.Collection[typing.Iterable[Survival]],
-    ) -> float:
+    ) -> StatisticResult:
         """
         Compute p value for survivals being sourced from the same distribution.
 
@@ -127,7 +128,10 @@ 
Source code for gpsea.analysis.temporal.stats._impl
alternative="two-sided",
         )
 
-        return float(result.pvalue)

+        return StatisticResult(
+            statistic=float(result.statistic),
+            pval=float(result.pvalue),
+        )

 
 
     def __eq__(self, value: object) -> bool:
diff --git a/latest/apidocs/gpsea.analysis.html b/latest/apidocs/gpsea.analysis.html
index 2b10c018..70c2f3d3 100644
--- a/latest/apidocs/gpsea.analysis.html
+++ b/latest/apidocs/gpsea.analysis.html
@@ -103,7 +103,7 @@
 
gpsea.analysis package

 

 

-class gpsea.analysis.AnalysisResult(gt_predicate: GenotypePolyPredicate, statistic: Statistic)[source]

+class gpsea.analysis.AnalysisResult(gt_predicate: GenotypePolyPredicate, statistic: Statistic)[source]
 
Bases: object

 
AnalysisResult includes the common parts of results of all analyses.

 

@@ -114,7 +114,7 @@
 
 

 

-property statistic: Statistic

+property statistic: Statistic
 
Get the statistic which computed the (nominal) p values for this result.

 

 
@@ -122,7 +122,7 @@
 
 

 

-class gpsea.analysis.MonoPhenotypeAnalysisResult(gt_predicate: GenotypePolyPredicate, phenotype: Partitioning, statistic: Statistic, data: DataFrame, pval: float)[source]

+class gpsea.analysis.MonoPhenotypeAnalysisResult(gt_predicate: GenotypePolyPredicate, phenotype: Partitioning, statistic: Statistic, data: DataFrame, statistic_result: StatisticResult)[source]
 
Bases: AnalysisResult

 
MonoPhenotypeAnalysisResult reports the outcome of an analysis
 that tested a single genotype-phenotype association.

@@ -175,6 +175,12 @@
 where both genotype and phenotype columns are available (i.e. not None or NaN).

 

 
+

+

+statistic_result() → StatisticResult[source]

+
Get statistic result with the nominal p value and the associated statistics.

+

+
 

 

 property pval: float

@@ -185,7 +191,7 @@
 
 

 

-class gpsea.analysis.MultiPhenotypeAnalysisResult(gt_predicate: GenotypePolyPredicate, pheno_predicates: Iterable[PhenotypePolyPredicate[P]], statistic: Statistic, n_usable: Sequence[int], all_counts: Sequence[DataFrame], pvals: Sequence[float], corrected_pvals: Sequence[float] | None, mtc_correction: str | None)[source]

+class gpsea.analysis.MultiPhenotypeAnalysisResult(gt_predicate: GenotypePolyPredicate, pheno_predicates: Iterable[PhenotypePolyPredicate[P]], statistic: Statistic, n_usable: Sequence[int], all_counts: Sequence[DataFrame], statistic_results: Sequence[StatisticResult | None], corrected_pvals: Sequence[float] | None, mtc_correction: str | None)[source]
 
Bases: Generic[P], AnalysisResult

 
MultiPhenotypeAnalysisResult reports the outcome of an analysis
 that tested the association of genotype with two or more phenotypes.

@@ -226,6 +232,13 @@
 
The rows correspond to the phenotype categories, and the columns represent the genotype categories.

 

 
+

+

+property statistic_results: Sequence[StatisticResult | None]

+
Get a sequence of StatisticResult items with nominal p values and the associated statistic values
+for each tested phenotype or None for the untested phenotypes.

+

+
 

 

 property pvals: Sequence[float]

@@ -273,6 +286,37 @@
 
 

 
+

+

+class gpsea.analysis.Statistic(name: str)[source]

+
Bases: object

+
Mixin for classes that are used to compute a nominal p value for a genotype-phenotype association.

+

+

+property name: str

+
Get the name of the statistic (e.g. Fisher Exact Test, Logrank test).

+

+
+

+
+

+

+class gpsea.analysis.StatisticResult(statistic: int | float | None, pval: float)[source]

+
Bases: object

+
StatisticResult reports result of a Statistic.

+
It includes a statistic and a corresponding p value.

+

+

+property statistic: float | None

+

+
+

+

+property pval: float

+

+
+

+
 

 
Subpackages

 

diff --git a/latest/apidocs/gpsea.analysis.pcats.html b/latest/apidocs/gpsea.analysis.pcats.html
index 92599f41..9c12fd05 100644
--- a/latest/apidocs/gpsea.analysis.pcats.html
+++ b/latest/apidocs/gpsea.analysis.pcats.html
@@ -129,7 +129,7 @@
 
 

 

-class gpsea.analysis.pcats.MultiPhenotypeAnalysisResult(gt_predicate: GenotypePolyPredicate, pheno_predicates: Iterable[PhenotypePolyPredicate[P]], statistic: Statistic, n_usable: Sequence[int], all_counts: Sequence[DataFrame], pvals: Sequence[float], corrected_pvals: Sequence[float] | None, mtc_correction: str | None)[source]

+class gpsea.analysis.pcats.MultiPhenotypeAnalysisResult(gt_predicate: GenotypePolyPredicate, pheno_predicates: Iterable[PhenotypePolyPredicate[P]], statistic: Statistic, n_usable: Sequence[int], all_counts: Sequence[DataFrame], statistic_results: Sequence[StatisticResult | None], corrected_pvals: Sequence[float] | None, mtc_correction: str | None)[source]
 
Bases: Generic[P], AnalysisResult

 
MultiPhenotypeAnalysisResult reports the outcome of an analysis
 that tested the association of genotype with two or more phenotypes.

@@ -170,6 +170,13 @@
 
The rows correspond to the phenotype categories, and the columns represent the genotype categories.

 

 
+

+

+property statistic_results: Sequence[StatisticResult | None]

+
Get a sequence of StatisticResult items with nominal p values and the associated statistic values
+for each tested phenotype or None for the untested phenotypes.

+

+
 

 

 property pvals: Sequence[float]

@@ -236,7 +243,7 @@
 
 

 

-class gpsea.analysis.pcats.HpoTermAnalysisResult(gt_predicate: GenotypePolyPredicate, statistic: CountStatistic, mtc_correction: str | None, pheno_predicates: Iterable[PhenotypePolyPredicate[TermId]], n_usable: Sequence[int], all_counts: Sequence[DataFrame], pvals: Sequence[float], corrected_pvals: Sequence[float] | None, mtc_filter_name: str, mtc_filter_results: Sequence[PhenotypeMtcResult])[source]

+class gpsea.analysis.pcats.HpoTermAnalysisResult(gt_predicate: GenotypePolyPredicate, statistic: CountStatistic, mtc_correction: str | None, pheno_predicates: Iterable[PhenotypePolyPredicate[TermId]], n_usable: Sequence[int], all_counts: Sequence[DataFrame], statistic_results: Sequence[StatisticResult | None], corrected_pvals: Sequence[float] | None, mtc_filter_name: str, mtc_filter_results: Sequence[PhenotypeMtcResult])[source]
 
Bases: MultiPhenotypeAnalysisResult[TermId]

 
HpoTermAnalysisResult includes the HpoTermAnalysis results.

 
On top of the attributes of MultiPhenotypeAnalysisResult parent,
diff --git a/latest/apidocs/gpsea.analysis.pcats.stats.html b/latest/apidocs/gpsea.analysis.pcats.stats.html
index f67c3aca..4a23df55 100644
--- a/latest/apidocs/gpsea.analysis.pcats.stats.html
+++ b/latest/apidocs/gpsea.analysis.pcats.stats.html
@@ -106,7 +106,7 @@
 

 

 class gpsea.analysis.pcats.stats.CountStatistic(name: str)[source]

-
Bases: Statistic

+
Bases: Statistic

 
CountStatistic calculates a p value for a contingency table
 produced by a pair of discrete random variables.

 

@@ -148,7 +148,7 @@ 
Supports shape
 

-abstract compute_pval(counts: DataFrame) → float[source]

+abstract compute_pval(counts: DataFrame) → StatisticResult[source]
 

 
 

@@ -170,7 +170,7 @@ 
Supports shape
 

-compute_pval(counts: DataFrame) → float[source]

+compute_pval(counts: DataFrame) → StatisticResult[source]
 

 
 
diff --git a/latest/apidocs/gpsea.analysis.pscore.html b/latest/apidocs/gpsea.analysis.pscore.html
index 93416cc7..c75a2d87 100644
--- a/latest/apidocs/gpsea.analysis.pscore.html
+++ b/latest/apidocs/gpsea.analysis.pscore.html
@@ -164,7 +164,7 @@
 
 

 

-class gpsea.analysis.pscore.PhenotypeScoreAnalysisResult(gt_predicate: GenotypePolyPredicate, phenotype: PhenotypeScorer, statistic: Statistic, data: DataFrame, pval: float)[source]

+class gpsea.analysis.pscore.PhenotypeScoreAnalysisResult(gt_predicate: GenotypePolyPredicate, phenotype: PhenotypeScorer, statistic: Statistic, data: DataFrame, statistic_result: StatisticResult)[source]
 
Bases: MonoPhenotypeAnalysisResult

 
PhenotypeScoreAnalysisResult is a container for PhenotypeScoreAnalysis results.

 
The PhenotypeScoreAnalysisResult.data property provides a data frame
diff --git a/latest/apidocs/gpsea.analysis.pscore.stats.html b/latest/apidocs/gpsea.analysis.pscore.stats.html
index 429f0e56..df00422a 100644
--- a/latest/apidocs/gpsea.analysis.pscore.stats.html
+++ b/latest/apidocs/gpsea.analysis.pscore.stats.html
@@ -104,13 +104,13 @@
 

 

 class gpsea.analysis.pscore.stats.PhenotypeScoreStatistic(name: str)[source]

-
Bases: Statistic

+
Bases: Statistic

 
PhenotypeScoreStatistic calculates a p value
 for 2 or more phenotype score groups
 computed by a PhenotypeScorer.

 

 

-abstract compute_pval(scores: Collection[Sequence[float]]) → float[source]

+abstract compute_pval(scores: Collection[Sequence[float]]) → StatisticResult[source]
 

 
 

@@ -126,7 +126,7 @@
 
See Compare phenotype scores in genotype groups for an example usage.

 

 

-compute_pval(scores: Collection[Sequence[float]]) → float[source]

+compute_pval(scores: Collection[Sequence[float]]) → StatisticResult[source]
 

 
 

@@ -141,8 +141,13 @@
 
The NaN phenotype score values are ignored.

 

 

-compute_pval(scores: Collection[Sequence[float]]) → float[source]

-

+compute_pval(scores: Collection[Sequence[float]]) → StatisticResult[source]
+

+
Returns:

+
a tuple with the p-value and the t-statistic

+

+

+

 
 
 
diff --git a/latest/apidocs/gpsea.analysis.temporal.html b/latest/apidocs/gpsea.analysis.temporal.html
index 90b3fe66..02fb33c5 100644
--- a/latest/apidocs/gpsea.analysis.temporal.html
+++ b/latest/apidocs/gpsea.analysis.temporal.html
@@ -139,7 +139,7 @@
 
 

 

-class gpsea.analysis.temporal.SurvivalAnalysisResult(gt_predicate: GenotypePolyPredicate, endpoint: Endpoint, statistic: SurvivalStatistic, data: DataFrame, pval: float)[source]

+class gpsea.analysis.temporal.SurvivalAnalysisResult(gt_predicate: GenotypePolyPredicate, endpoint: Endpoint, statistic: SurvivalStatistic, data: DataFrame, statistic_result: StatisticResult)[source]
 
Bases: MonoPhenotypeAnalysisResult

 
SurvivalAnalysisResult includes the results of a SurvivalAnalysis.

 
The genotype categories and survival are reported in the data data frame with the following structure:

diff --git a/latest/apidocs/gpsea.analysis.temporal.stats.html b/latest/apidocs/gpsea.analysis.temporal.stats.html
index b24a0ccf..59a4ba0f 100644
--- a/latest/apidocs/gpsea.analysis.temporal.stats.html
+++ b/latest/apidocs/gpsea.analysis.temporal.stats.html
@@ -105,13 +105,13 @@
 

 

 class gpsea.analysis.temporal.stats.SurvivalStatistic(name: str)[source]

-
Bases: Statistic

+
Bases: Statistic

 
SurvivalStatistic calculates a p value
 for 2 or more survival groups
 computed by a SurvivalMetric.

 

 

-abstract compute_pval(scores: Collection[Sequence[Survival]]) → float[source]

+abstract compute_pval(scores: Collection[Sequence[Survival]]) → StatisticResult[source]
 
Compute p value for the collection of survivals being sampled from
 the same source distribution.

 

@@ -127,7 +127,7 @@
 A two-sided alternative hypothesis is tested.

 

 

-compute_pval(scores: Collection[Iterable[Survival]]) → float[source]

+compute_pval(scores: Collection[Iterable[Survival]]) → StatisticResult[source]
 
Compute p value for survivals being sourced from the same distribution.

 

 
Parameters:

diff --git a/latest/apidocs/gpsea.html b/latest/apidocs/gpsea.html
index cc9f64bd..95f0853c 100644
--- a/latest/apidocs/gpsea.html
+++ b/latest/apidocs/gpsea.html
@@ -114,6 +114,8 @@ 
SubpackagesAnalysisResult
 
  • MonoPhenotypeAnalysisResult
    • 
 
  • MultiPhenotypeAnalysisResult
    • 
+
  • Statistic
    • 
+
  • StatisticResult
    • 
 
  • Subpackages
    • 
 
 
diff --git a/latest/genindex.html b/latest/genindex.html
index cbacb570..aee3971e 100644
--- a/latest/genindex.html
+++ b/latest/genindex.html
@@ -1135,6 +1135,8 @@ 
    N
    
         
  • (gpsea.analysis.pscore.DeVriesPhenotypeScorer property)
 
    • 
         
  • (gpsea.analysis.pscore.MeasurementPhenotypeScorer property)
+
    • 
+        
  • (gpsea.analysis.Statistic property)
 
    • 
         
  • (gpsea.model.Disease property)
 
    • 
@@ -1309,10 +1311,10 @@ 
    P
    
 
       
  • postnatal_days() (gpsea.model.Age static method)
 
    • 
-  
-  
+  
-  
+  
      
       
    • statistic (gpsea.analysis.AnalysisResult property)
+
+      
      • 
+      
    • statistic_result() (gpsea.analysis.MonoPhenotypeAnalysisResult method)
+
      • 
+      
    • statistic_results (gpsea.analysis.MultiPhenotypeAnalysisResult property)
+
+      
      • 
+      
    • StatisticResult (class in gpsea.analysis)
 
      • 
       
    • Status (class in gpsea.model)
 
      • 
diff --git a/latest/objects.inv b/latest/objects.inv
index 1dfd0089f83d55d1e680e5d2fec0fc3169253eea..481150d76e106b2c4cce673ae5f280c3f8813ab0 100644
GIT binary patch
delta 8151
zcmV;|A1L6^KZ!t)cz;WC<2aJO`&TGpH#T+;(#%BcZcNNgCDXRHt;a~RdulESnuH`y
zQ6!t7R964`1qePsiU2`8c>0VEQM#OshC=#G->-%hcA4&ms}BR2{B*h7Ch
zkS~*Cb_)NEejES$X#7Bbbt5;tq5ugpmPvXLCez{{8;H(fMt=ak&_!tU7a?9R(BzPT
zB!zz9xfvv=Ng5|G&92(OD08y_Wr3%Mx`?BAeS}e*T@z@m5(KD|$LVegW~9jk29_wqcqPuLSm6%{bHHGi%&@iGYC@X#i>uV9A?MZH_PL@nQKjnCQ13bMT(0X
z+C#588g7TOTYo4w1I`~<=xzeoi5rH%i_cMpH0wx2f)x~NX$E~j8p9^jDf2+V7Q~T7
zq6nbi5CwZ|x}yy2;}p1Ia&&DqKju3l_alTBiB7MihqvVpU;%b74yJzn4rVX&*T*}s|1w{%=gVhO4bEoz3U$X~?L-7d$58~M^DexhME>Xbj
z=th84M?U2>FGA%9*c-8KDJH95tk|RuCR@gWOJ&z&bkN#YQ31)k(^=T#XhvI
zBY%_%_cTN!FILH?5LmE4Z+{3*!_acq=_0YFxB@b}TH8r%Uu8jXNRl#uy8_a-nQE}%bg|Uk&JAUeAA7aGSRdP0?oB-dnGffiAMK?XcH>!57A~-*(;(=sv>}E3Tt`No
zzYRHr-`w7aZeXD-eWSYRjT$^@+G613daXxtw25lg@~%Fl2|<4bLEg+zC5p5R_Z3D29XcmToMs51
zqnivGJLM^#0(69_^XYoot_Z>zuEQ3C^-65>-J=$PSRcpoMDp4$BM`TB&3{PLhQAew
zJz~;p1j@v{CZI~Vj>GGk<>=GhCWSn9zMq2p;}EBTq`zZ?>v#Dr5=IEG_hXU{7;Dhw
z8*oDR14{eJ%3RTX+YFsgCl_r=8yz4BVRXojUm*be{0egMSF@p^IgKe*h6c
z<+|Kijuh^{&?uzv@I|`FDB@RDeU`cr^3ov5zJ~q$C8aL9J)oog7YYFPd+23fDZvkT
z2Uj4Up7l7>*nRF
z5AjH>lW6shk056Zynp6xJ+^86z&%7UB75}jNqdT;_)E%*;OAWk8<)<=M}ewr@?oGl
zOR*q~6&=CIgKD9JmIRvA6CYB?LVov)ElIRv?S|zUun*6c2m^0MvL{FW3%lE-*-&3B
z-tb72VFB`ilWc;&pU%7_@jdMaOLu>p(O~}~JJFEgYufqV_J5$s{fDpt4Uz8E?;E6F
z(ATRCOS79Ax7_VH%=cErN(}WS9+Sj>jN<=6dgM^yuJ;j(5=*$;|vLi2#R!MY?V3&sE(($f3Fa9k*ds6NcMdV7EfJAtTp>W7-S*>H0A~4%x
z$q9ygNQ1mMm4BPB=P7%q=rmOxA`7BJ)h=7|v(!EfhGsCnf)}ktw@>2}*)EV?fp?bP
zIj2QAz(dmFsrABYaa24%DZ)qiP8!6P0(QgO(mxK{ed^4#DsWh=X~F_K4d)b|u;*k;
z8~7BqG(y0b8>LhIUGfSDZQgtz>Yd7XKOHfx{Q@TDzJHE8l*?LwYZ47PKdb>SK0yo&
zH)6L8@&}2vNhYnLrS~b@BnjgTe8ivR|Hu|+YN-m1_vJSH&(uxw_P~w~sQh$ebabnC
zPwyH_kqqj&3i1p%>Zm9c_sk<#w$z3=DPICSpX{Fp=}5u@7fRIU7wZVb!RE@tI4M$I
znvQG&e1D#N^5;95^pX=~ns(tv(XYoKi{N$8InNtD6{6us6$jHcYuauRIb3%r<&K;V
zv|G3)#U087WE6BffN*d(kdm)g!AyzBBa)Jmry!<;YvJF>l)+OHr-iEY*s?NhpB<~x
zIgy{lK_uh%HnC+uD^16?`w~cMyFAU7K{Y0O34cm9+*?q;{a2T$2_DJGEVCjB#QZMuA-_QOp=H^OdK08fBy7cr+|H2rD
zO@EGtEw5l}dVc)65~=Ks5DheAu|r56R0{x~K+m4EBuG7|UKT#OXK0
zbf*$FtlA*gwTo|PZT3o+Uuo5;TP6i#2}+UZ%~FDXLlbbiN%3(uoxM1~S-umT{2|!C
z2vBaaKRQp-x7Qt@Fze~=MGc4U`t*(v_;(O>jYvfC(;t7$X-4)HAoCxMNl+D%fEAKlYW~X1l#wR
z>>c?gkJIm4FkgbjYDu+;Kb??7`qgoMF#`16nQpXz=G)a@|M$;-S?{z^K7v$uN`JQ}
zyYF7bcl7k+&sTK=6qAwwj1a`Wx-bWr-!>UX!XZQ+1eB#yL&6i~mPD$xM2>XDD2uQu
z)WX4CD8uunh@4Z##nY|thD@3ensr^{T%nt40A;}mhCu{Xt9ce5<1|w;STt*XopRxp
zE0%)+V%8$`!PpBe)$4{r$=rf12Y*$ccn5)RLbmcGbr9`ieenu3J)r#PDsaQ#0uA8!
z&?DOAn}8yoEq1KTXlx6!+PZ2I)L4(8xO;eVLnFmDg>#O6MDfoEAoytz?Gg~siBzsB%W(P41cXUVR7OMOhY$8`N*NBIxJj$0hO*`c)U$@8*En`K2&Wm
zl7BK=&0n2IK>nv3ZfN2y)~oHDypTS91>fe=tr6JA)nYnd8i87@cJn7ANE_!F7t;{b
z+L`W*K>c&RoPnqL^4ZxK!OQJ0%E%^B#U4}yXvuOQ9`^FE$@Hh2Dt{_34=wj}j)w~Z
zo*%h%)DoX1P-elFe-BggjuobGs{}Tv3Ic1zX%s+tlKsq_g&y3Z&(--;XEFch_vh7{
zy3Js)cFtyH3~jY2u)y>c123mL$0+K?d2%++a%KQ^xdOB4>#IIc`B=D)Lik!5;a9gg
z<>yP0drCsZILR%fwtuoCt+JsBJSEvxuQX_4s$NiW4$DmvWkX+MA&j9a(Y(9?cY9HG
zNn05CwZ45vm4?Eh>**s7O+j|tFlqw!=Kf5RphYY}1(Mm`uGGLxegl&_7ENdB!QzmM
zX^N-OOu(I^KpAIEBLqqnUF4m(2dGJ3#T|p+&QLRa)Cs8{tAFW))eY8^pk>?=dvdC7
zTnh^6wn!DSG}9UtoT(}^5&9{yB%Ym-Kw-}*8)(S3%Ib(#2aL6ms>7NFiYWOErwmdN
zJvF1Ored)rUa=~pQ$RLst%cKC(ow=X>P+dX+-ACP6OF7K>H_Ke3=9?m@dtwG1^Pz7
zG~>!OmN}`k;(yC)y0-IFKc6sMpBfMoFNNhRcEfd`3Dtg4LBD{LpqRB7fXZU6$XkK7
zfSH@`w$!Nl5@X`WCs%o)t__y==dua*srUuDp}5$8Bg=~5Ur04H*M=nlxk6f0EvlAl
z3}z_$ZzUN3c8al$GbC8+2@+&V#u8Vty;mf7fVK3i9a8oaxqi)Ws?E
zLm6hr?0<wX@9kxPXTo7lP*WjUhC{y6%xde9q4^<
zAr}ziaRZ#Q)Ogio#}wMa*AG5%a8c2sMujzM^jT!R-E=i3S(8-XPt<{9Zji4bjac&c
z`VrK@B^rC^M-yvSE~2Yeehz@We|6`!
z34ipqHUl(YZcPEbn*myw0@|7a+HI!G?dxim&vdjQHJznfn2D>t&!7YC<^gbHxY*tp
z#MAH%JJ51tc=7fi3^JIi9)A@9(@jJ4W(p(7jaRabq2dAGV72NE^c{d&&U*)*kzG;(
zT#b!V1*%g$KdfpiD8gj6dYmtx!Pfcv8-Lku3f`xi`Ex8=+z@ci8Y>&<-OfVbVobaiZ|3upT>f7%%ao-fHM
zj#p=gYsA?s=Hw&?)|=JRI8R;#fE^;oV5OI^*sF0iMsaa%V6~pljMu|%W4v+~RDY!x
z^UZQ<8hXCnI=FHT!!8$(AosFnoB7(bPA_o<7q*Y#aQLU72_W)7j1rlbs6MO*cF6y4sor+&H@_
zu8v3J(yrFvIY%~$Xtekk&sOQb<1yp=f*b=g3%q;!wl!_KDW(N$y?X-R=1V#`neR-S
zq}|KLvFC|11HI|$W{@pZ`rF#xY%PCb(8#oxJsgE%5cnXA$u96Dbgx<=kADK*5SsF7
zH75V$=pukFRkT`5m>jH%Z8SrUdcfwQPW15G#YA}C+<~`Fz-IlKg4GWV=`DY?LCma|
zkOK%Bd##xKlj1I^>e_5I%ftX;-L39h(<~gpV((lt0LN@^(?zQffGE{jaV2}_X4A0%
zhr3m^6Q13nDUFIVwZJ@je}7T?l15p?B40P?&GAWD)G}i?Y`cF*m!9V92JP&5vdC=a
z7W^UWxZ^<^*0W4C7y{Uqmhuw!`ml?UpoyVeO(b>#ghK_Sx(&~KVv}3XP
zt@|P=S#&nD7=NcEJ)4<>&pW6jT|v$KVwT%OIRj}bfEG`6DSYF8ZGTyCl8Fa+yIoio
zwaVFs{_NX9D9z9b)1oVU8<`u4q}7TG#o^{&Zz0Rr2H^0Bw?PlDRtBY)vBM=DPFRC*
z_-=MXNsn_yMlo({x6eRun!ATVN8vj##B6HX#%AuvS8Vhfgl?vCvodc{d>~zsy~#y(
zu@$EfMeiEWWWwhSihm@tILhb)9HMCuizfske|@;o58!&9#3Vr;SMuHydB7Cz5&R7p
z$31(*M#GsM)N3gu)4uweOV5<^3GF}PAPvC?6A-7j`Ai<#R&%?0i
z4QO+1S>xVE`pL=tSDXSYK0JMdSDQ>px%1Z$LEvqw?OrAtpnt^66<+G(xe_up(T3}Q
zT-1}fkq1E*n-?2KK8Pa{h;<|1Jp8b`a|grcd-!b1U*no?)%+TIb7C9oFBUpV3zEE6
zV-VJG_o(}YnN~0G0tDo)YLtgG-nZCJWv1}kO20L=k^)VZ4%xCPcXnDHmEJXN8Wp#A
z1P^$!dokj+)qkkC`vitj<0J<)2`PQEr8Fcor%2E@YT5I61Fk{$BZLNIWZ}rVa;ZiJ
zhl@5vsQ?x!O0~5`VR%3VoT>M?ACW(S7czBDBGu?vC|S;~X^%EL1KKagt=F%?Ux5jE
z%@E2kwTD7ArUFHR2^!*pJ#5{!PmQsG)ybL_DIl|zLVx&vtEj&xDa5wlg9w$!ox7uT
zjdYxFT{8_`3Z9WuvaukF&;cxkI4M2|?A!q8NBVFpvm|h{9$}~uQcRQL+%7azI$LG2
zFF7`2u#U`cVR{KXXhil-kg);6}gFX?WPDCDnc(!`8qVY!4(Og@iR+nt2S-u0T10;A#PUxo`T3X
zuM!-Z$sYeta!2V9V)n0hHw^rIy?IkzqOV^x5kr2F?~gkaWs;C1;NqyhF)n%^WAM8v
zE1JgH%=M1=-{l4rlfxSy-t=fdH__C)8VIYoGJo7c=eG*A?lrMhj0wWF2U=sZ)$q5_
zh8w+WlaR?m2=J+kW~LZ#^kQR+ts!JE+$dtM-06_L%6S0m`}@n`f@}_>LIz7C===Ku
z+x)W{E-u!^TL=
zm4C;nJu<>#O$>cglcB;!*ziTVq3!r094K(9D
z<>3KyWFh`@8hAt3j#QcodGishQ~5~wUS-D)^aNPH$Zh2n`N}k6vnR4j&xujgfuQ;
z2fd1V*?`xO`g|u%-Q{we}9S-7?JsOd`^4Xrbg<5$lzxNf*2g#$PZy26TrG$
zKFMJY^k*7mDxjAD{uERb`OK-N{1f$?3zPPae-XvoYOsD3iG31%aGKI+i&5O|p)5xu
zzm6bJd2A|E5~9jmMz~zm{{Sr)?V0>@1Cz#;JSw>-MBkx`2#d@k7uq1@W`Ah{=(J1W
zQ|k7fE*KMH1?cRC!SCX85JONVCpY~8Q~LUo_?+?}*w#a|dya)GVM@F;qJ(>5F4{4J%)I3!dn=$SzR8Ln^5mZqaQU*LO=xOPpby*+6o=;w
z8sXBi#1+QGPu-u`13wtB!+#}Osl|Ta9#Z$Df?Nz0I(|VL!ialNfY#x3t=15r(V8q&
zNokOzmlbyUGh;po#}#TK@2fiPXdpT8IwKF7uL5!mH~E`HrIKFQt}ApbDf#LT#?
zg08K^dQ;l$Gm+EXL3P^+)g->;&K?p^!{kW2AcSN(EFyT$v`G%XnSZ&PfHwn>V`$~>
zrVxAf!<3HSBGpE2a7<$0Ms9dTfjDH+v}bM@LOiFZud$-c|654zWhL^R5lqL2bKt{2
zB`Nd+kN7ixqUq^?TcSLt@i`fNTu1cdDF67-V9lZNpSJ}k7$cg71bo~BZ04L)h2lb#
zDHyCeml$+%$~+PtBY)*S&cGBo*>zw%^xYCdIw)<;|_
zj0|m=wwtszL#MRyn;ZZzYxBtu8R_;;e8a`N;J$NgNa=RFb&NBb1;jBIGB;`5^W6k0UmHci9@(KlVT}XVOPqmq&IIG>@!v
z8E%(3Mx96AJ2~=Y5H57JA~0f7cUEk^PQb;f+=>yqs?ZXM;&y6h@rgoA*Yi>SzBr6L
zoco-`C_cF%NPl5o)C=UgDjjL5n^Juk*C6G!-sAcf>sg$pFf1Y#K{T3{*+!cxTj61%
zhmRolcmi+S9PoO4sOt3y{MR8)ucaULt%Ms@iMuGqhirTxE*COPHmXK93jaVK{2kLE
z+&JEk-Dq6+cs%Aq7$fA?G_xFHRK)S({m6|9HxZ-9F@J*N>=VQK<6_dr1rDO*oQ+A$
zu7)Q0N7)hoSIv_~`K25M7N*0N6KfI59_TXiIKjSofHI<21E|(CSI$L&MtB}Q!g>PJ
z2l{yWxF8^}`i>jxmjgfwo=9V%Lpe0kUh=!kQ`
zPuI)FxJ3NP3KapDx$=#Q-cq6GP@^1bltcaJle7D;hkOqtwhwqFg&EQlzvYUQ`J5|H
zS#$fG-r-DXiOoh*qlif;Pp^a
z>wjS}^fD^=yxuxfnqr*cuMNgJ9mbqT*clAz2s!$X(GHJ~cz_8X>RvpcqtD4Nw1WpM
zZbQiW_p-axzuabHq;6$w3I9+JYuK!hD|ch)2=`hIZDe$)V9HVM=P}44cpaYy
zo37l%S30~PV82qZ(c5T81~%+Cby%3>I)5%d&{|v2-5u1{oZ=`p>bfjyKt|)Rp3C%s
zMRCwEuN>mXdc+CKqgMoCT>m-Fon8N&3QUw7@Tf+5sJpHlYS~@U->45lkZ}v+A&U+h
zS)30m53N>IZ}!?f&3|tLkLxL)5_~yKBu$#!|82X3RT?mCwCKu5`D>{d#Ja@H5Pvd^
zv0=4Xl)7j1beZ)vJ7P^~^qk*F6h6C-$>q0c91gH`f2TP|Ma~C2he)x?Gyv#tlzmIT
zugUxg9pj&+gIO(EHF9Q!9WL3n)eRrGTaJo6g-t>aD1lzEzfw16(0H|_IY*^~RE$@W
z8rWzP5<|yMHEx!0RHk@9=kyX>+<&kit4vv!xX4-gpjmpxO66i3pPmO8^c~JNBH2bH
z+e2Bi?4Z=B?RpGsB;__ul^n}J1{;M|AcjA0Sn6cfi3Iw{)chMcxsm_=z-=YAxZ;hEbj|Lb
z-tyJE5E`Qw>!&vj5+{FYs)Vjx{{kZiU9=p@S&S4$Mfz#j@JTy((lh;(0B_7xyXL9V
z6YzdA-mJZI&Mq<4>}R~4nNYUor2_Y@ADwmA`UL0tu0jT`=i2S0aw7-*OsJZTv%v+q
xiC8~+=hUsHDqY0#a}V#38obRzxyvWlnA+pOOU_E$Q;Xtvc4E=N`TsEPA%k!(!lD2G

delta 8094
zcmV;PA7S8$K+r#scz;QA<2aVS`&TGpCMISMQg=tpOmy^3Dbu#5tfeK{)!7#WO+gYn
zDUwA{N~?bTVBrEv1PEf0>rhc?5%|6b;NjunVcVw&`h)cHw_~zBMR4%vfuDxkBtU=K
zlP{w~evJN&eH;G!VEDj(^44x7|C
z2fHK#ev}@3quwFsJ0brgf)0yB`$#=bAlFpncc&zdb&Xemsz4x&arHsuOcC-V_alIt
z$F#?S4q$p1t{E^L^=om+>0R7Ap^IUdD5>TcC`qHG%5b@
ziJylYOOeD7?8^cE;3M!m%#wQxktPU**aO59F@G|YxTZtN5rP2X=>aM5K7&3{!2ICH
zfK&&aGuRiQ8aLgIShp0T#V<~5QVWwSV|
zR)4MXw#&3mVSwl8aJzxo5xE;w1Uw_+kgu2CWcoDq9^EdDj{nJk3r97}CTCL-w;Pj0Mi$kxhm
zBN&YWs|0hoK(aWF%Mv|?_(xO)lND?*2QEa#otG5GEvoW7LmQiGqRM!8kHA*wIJ@nV
zG44IDQQ>M|sIb&h?cj7bfuC{Fv@-(D#Xxr@v#N}yCVztEx3=f8&R!*6d*
zza3aAOV{XXdxL>U8b3{=3uiI|K72+EytPo!A$D|y%HGiO^8(|{<
z11kHg+FbE{+YFtKM;~*+JJGOBMUD$quE*G902o7LD2A#GiWW#B#-2ORpl%7vT5!-Of{apM*e+bfHeaC$f&xF5@@Xob-
zL*L&**q}vsuV+MJl3!3zoPYZA6|}*@kM|HnFy7~fuMhx!euX|G@(F$gZ-}s8l;J85
zk2rl0A_&m=iv&S=b_()S=0{+Q4f@xZmTO7Q?E6;;g5A^{hB4SdAIk#&03v|Ob-A+~
z8QguLQOMx_i*%7w#ILIQJo94|WMP_r4g2X!N?mk&z()Ho6aemaFn`FuQi31w4z2*5
zo^?3W!`|Gw{=2foVn^JCus3W(lbphiMen
zNsM~OM@SjNpm`mLYuat-@8blKz4G^@JtlGTCFMo%^DcyqTP@V1Kvg#NFi@SPSP;gF
zj$j->z0kpx1cub3Eq`Q=h59ZOSCSaV+AYh|V?UfL5qe&|;!Y0w3%~25*-&3BUjImx
zWdZ2GNj9V3PiJ1z(z#(
z$xV$r?)C!adn;lkhW-+dP2xXB@&6z_vafKL`-sJe6U=6w~z5|1a5Hk
z5wg=bxsg{yt0lTYu**Pl<#<<}7ym}jfRsB$5xLqWBoUrsDC{#^*6UcM2;8<`tXidQih^U{5&cPiukbi}syOPIKOGwx6>XZ@{7)aM+p0lfSqFRStV_UsDde=~i
zq*u??kf+B{M@^}OXC8&JWiG_Y#1i27WcNJCL=q9WRH81w*hC-!woo3fgZi^`3x4$SEpHXsMcgJLCJ>u0LBQn(^m18O$`$K-w8T{?=gGR2XCFb
zxoz;?Q#MnI5#+i__e|TEj!x8m_-W+F*v$%IMt=g-XSD#eIyv>SZwxAx7JAQEa`)0Ib?GL!PKQ)SpfpPioRUKkUwsnM{-
zXOP4Q=I-g}V-8NKlxH{19Lf#EQoknql^_35ynLmNsuxFZ&sdMK>;-+CeoIVuDq+K_
z^?!0*+xYs{W~X%YN~>1gvMCr(P>RHEmXh=vmO#)=ijR}=@_)gnUSi-Xg0dMJ{Vu3Y_HDeEY~SOux8xf=
zj=!(LbPi^VInyTbbV3p7SI_&!3eb0NyfOlst`~p(-#`ClxiLcd2s7y^-Hz;A|02Jm
zrz1aI)eTWXN&+xKm~8ch*+cqJauQ325OokxmQD`|Pn54D(yb+Oq$@#rj7^~t4u9@K
zIi5Ggtm_)*0{zSYC=ZV?3S+2S&6DJiWVx2XVp-|6#)Vt1Sq=_}
zTZ=FU<1e(-uNwxXavQZ8RDI$dgj*Z3l_#mgc$b)qSD={z(W9%tkHRywfU|`G(XOox
zDB{^-$I6bzUSU>SS8ak?>k$lh2Y-)#WTn`)a8B`$IQba^1V1gJokL<=$!K=6A>_|6
zKLCFZ$u?j*D#19YkGk6czlm&UgHj)bw|&}3WM%?CgXpw{+s?Ng)!+)bO4DbART{pJ
zOUEq|-Ea}^Zot||R-qLa+*m@hVwx$MHKRh&ZVtqlVX~{xOGT;F&R~>m-hXz&Ac@xG
znii)x0;Aw*A#glC)2H{3JI01X^PajpHTs$vV}SzPwY~u
zDfWuA8j8zL;<*;YFsc(CCpp6`@>4`d4n5W3;pz*hOa;T^ZD!hFo8s`HZiA8hqse0W
z>OBJTKkaZs6K}R$tf%Cq@_+Fw_%Yvm31UyaW&)&)k9<{$HC!0hydr%ReCCh<$*rQ>S@lQX~R9+Dp^>hyVGXlXj_SvW<
zKTDv^f-V0JX5>97OyO4vTu>DR&Wh70fc7N&nL7*JyG5U?^QYcy`hU;w&x<#Go55ji
zyw$=Q+G18p%8rc6hDPw1<`=WlppmV5LB%;NKTWj_eT{`MhOR`@@&?@XS=%MO!l2js
zb{$pf3x_Vpk0i1M*?)4ws14Yg`!j8V7O?~!NN#((Rs(bSEllcoG?S?Zk3%k|DIU1A
z0e6Z+ZJZ^G5NK6&k$2?pp&@-0cMN|!LBsG-E2Md>rWMvSSW|+QaZBvU>AG=OP{_1J
zs*t6f)~MiYRhf;@Pl=`Q?2G~me@@v#Ltd+_iD-4e*chogtbb{th>Fi)svs57Q#;CP
zD;8Vg6{|8P1?0olMmSeXI$BrtuC!?<#d
zWlt)j`0|pi?L5`bC-m2+2E-`HVEKw&e;sH-UB9ScUcgaU%vvl!<%v<`tw5W>+^4%O
z4XVDx7;TfIuYbKzcMV4SbJ+yDO#T90UtH|Jk!3~jFQglqyM`qJxk6f0EvlAl40b5G
zZzbsgc1*C1vn1Hn6C}u%j3ust+af@$A1bkd%GQ1?Rb~cL=<5!LYZ~r(t^C>EU780l
zQ@C3sz@8|)m=_H@$GH#8#A7~L{|bViqbF}Re$@}h5`PF|fVcTC^Tn@ou=f68goB+5
zww+0{RTzXZ0B*uFcD%MmAjQ5VO^nJX?ynOx>uCHseK%-S2J+}lyz$z5G{q_OLmOtp
z?TPJOA!X*#v$x)i*@CaJB%|eGy_t_UCQ#M3(Q#vCu73erfJ`IFt(euKrFGQQDk7Vk
zu$51%z<-4cMOGdFdHD}nMKAqvCAujK&sdtH{lrUKT2Rk|fzSjOEXB
z_C*>6TLcXD6p2BNHsG|wTGCt|lAd_O(i%CR66j=0x*R!sZL(`sN|3~Epm*V!TtJM+
z4RFdc>s6Bqk&~
zm$S%Q#LlYd1>4;fWPToKZjda2jrUcQKz6nym1z8-A49B3xrnY?`4j+q|N72t6XOe?A3THtGKu}uv$+i*6U%jvR=6}rqZ+NYCg6N
zJzcLoT)CEE=d(vZy{ySUjny(96Z^_vLpya!+wrCZ54~vT?)Yrh+!()dsvS)^-6`-e!!e3QdQNUY5(>|@n4!@mkgy-!Ycxwf0)}Jj{^U#pl^4B$poqzQbasa_#
zuN9YnRNN(1U7M|EnK(eKyVZSbhJ_B_p5G{k8e9=KAHb4T>a_B+l6b9I|N;k0%8pe|`Az58wxZ!X!Z*SMlBxb-)bn5c~~T$2|oo
zu!#Ch|M%?_Mq3Mw#DAfY_eZe2cHG#X}R;)5q@^3wUPmi<{sIysdjc+9hKcRZ5tK0cntS=
zvU|4Tw$-S(`-GNJlazwmgjBxSQW+B3QzW>xYT0SL0oS1a5kU(w@^EBbxl|*I!^Jg4
zsQ?ZsO0{)GVSjl*1%j#fup3c4ftND1P9pW_cqmoQwrP(sI|te=$F0|Iz+Zt$dF>FY
zFkKIYdQ1h10u!{v1v}WxwH;EJTr_}Qg(RhusKK!onB5I3uTPhq^ZuMz^9
z(GLGlaeqf?A7cKmcRvcZbiH|1U7~MZG#LZE$oIz`iZV*c5pa1_-x?RYk1_n+mKDvC
zeBuWO{O@uDip}9o3~zfhV4G;_T@8fQUKwto>8(On_nNpW#t32C1D&zCYWQ1d%Z=W)
zNyug)B>2olvr~*WcCoR;){rt-ZWK8ebvjh9a)0i@`u_g1KO>jJsFcCc2>Sj$!!|#3
zqunBKo2o76usp*Nk`Ys#L6nkf?;TSy{XUY9@;AKfky$R8pA`ePt68Fy!Ll)ubI~|;
zKt@=siP6^9WT>zaE_{)8Xg9uyfXk6D;?#8C*J#7kS=VWWCU;a6S5$aUPu^tHar>J&
zp?~F0+D^iT2+P(@K$T=izi}pz4ozp6g5OS1di%XOd6B|$Nde9&kGKvM&{e~@5*a#T
zr@B(K!%E~(jeqJ2)PXONOfgQPE0`Q!DwljhqAyS@u0#^0iJq=FGH{7ZodcGxJR)F$
zEX04#!l3Wkk*;)VGy++RH|<1=a=J1#;eR@~Me$;7ZEoU;*y|u{ucZKOsk%A(Nou{?
zgwXxua@GwMI7E_iCj+};t0p#7fUO{vEK+J{)vs{{(i9OO)!3J=P;z*IY}`R8m8r0S
zotMCO%O;&;8V){+t%x1u&gqV}B<;8&NzSSvKy7)X@G`NwVtD!z36R@`36gjh?tjV4
zd;wFt;*tRn)HYqXd8fzBgX3|GU#(;pueBVD{tZxF#daB8GewEN$bHJgNU{x#d=~8fqMwo!#$-O7oU)F#sgc?sa`>5pFaZZY-bRqd1h6ibPjc7;
z{h5Wi4(K_AKPA;fJ`1Xeeqw%eVSm!z@h`G?TMgEYqOeb*3(im)V=;=mJ+$R$aKEg`DBWrWK|-4D0hcc;x`bxt1a5)~M)zYVkJo_nCjxK`w?06TjdZ!isxPfY#x3qt=k1v6?JYNo$Z~
zmld}9Gea?mz!hpD@2Wa&X@4L!@H(RiTC4(U3^)0kM5U6R`K~KLv}b-4K|H5tud$+h`?rYP%Sz-sA%B<+_or|R|CDBM
z8wSLm`4dae2HX64GH-8d)Ul5stP59C{u7)
zbuKyR=$Hp2JVwk{H-4SCjf%(WU`=slsuYN(Yvp1HDm3)UUv)B?T1;7>brF{eqe5Gz
zZ6~deR4J=BM|*LXnSbO$)Y!_>RJW}55~seKRW47B-X#zUl1xbkny{UgVJI=FYaN$d
z!m6fs<*lR&ywwG!ZJZU3A|JV4CQZV^genr3d8885$f}~KR(vyqTnJg^vvmzIA^Xnb
z7dcos`3fye#7JSnqu`XS2=s)w7^J@balof^I?efT0g65HRA;ax5
z$DsAddn*TB1`$G6D*^*9b!)}abpjzym;C1*=)qm>|_^*AET}nUdTM0L)61Pzd_xW&7TrOmpY*3AE4E}*V_&a1lxM8vz
z`th*v@kGq~C_%`tX(kk6P{i?)-N26vHxZ*J34+7?6T@zY#iUIL9LDJ>ACj0|4NdY7
z@&o>_nkNnDr5ptoro)yKYZ1yH*fR1k#lCrna-vr~sDG9$7v*9=13Zr&U_F7^1A9Du
zSP+m`eTR+p%N`}7NCUs(AnzhSkN^AmWxyjoY~eWzAsW(=F;mfkB1cK|2nX-v@4=cN
zJiyO1!gfB#>LCQ<(p2IyDf!&x(D6X`U6+kY3)!O{p4i!;q7})Phh2ycI0yXngM5ff
zB%Z7=5r1%*E8nQ-EfqS28c?VKh5FAYZ}VRdbPpu94|pbp8M33e<%*Pa&P7vJGa>e2
z@UmPC=m!Ey_I7+WvC3bWwVRTEK9rqrcrCYnNhirMB{wHm{hD@;!&NV@i7S0kQK>Q;
zsDI#fdvx?E`Gs}xkjHHZS^r*k
zmw)<~+iaZFR~fH_f2fBwY}SXByU}-qd##2xGCEW+#Cua-4*?f`5*)tw=f>E*szf&bXa+~
zYDN8KuiaDn`!(>ep7LqIm%~Kbq@n)rwM$r~0sTgcwtS4gmWo5HOUw-+{TLfoi$|$@
zMn{)fUh)Ihlt$0_jYQ$|%aB}tnUX@A2qC$ml@(MPW4-^j@g`ul^hmH6Vyo3gzj+wvUi
z$EZ*jKA)D+lxB+if)zVD3CLRAXbEAf6Rqe%t5{oge$G1gvdywy(#78BO)Y&%9%2!p
z3xYAmftU7qsX&VBnX7c(Dx2jA@Y`pDEpx#Zn89gV1wrcT$CsgKj2N&BpoQg4#r^8@+Yv
sR#TNOV)?m)w@(e;=3(6BlNW1T?Frx&XQkIui{f{FV$s6+|6D)EUO+X{X8-^I

diff --git a/latest/searchindex.js b/latest/searchindex.js
index d5d27031..66ae53c8 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"API reference": [[20, null]], "Alternative phenopacket sources": [[34, "alternative-phenopacket-sources"]], "Analysis": [[25, "analysis"], [26, "analysis"], [27, "analysis"], [28, "analysis"]], "Background": [[35, "background"]], "Biallelic predicate": [[44, "biallelic-predicate"]], "Biallelic predicate genotype groups": [[44, "id8"]], "Building blocks": [[45, "building-blocks"]], "Categories": [[44, "categories"]], "Change length of an allele": [[32, "change-length-of-an-allele"]], "Choose the transcript": [[34, "choose-the-transcript"]], "Choose the transcript and protein of interest": [[34, "choose-the-transcript-and-protein-of-interest"]], "Cohort exploratory analysis": [[30, null]], "Cohort summary": [[30, "cohort-summary"]], "Compare genotype and phenotype groups": [[26, null]], "Compare measurement values": [[25, null]], "Compare phenotype scores in genotype groups": [[27, null]], "Compare the individuals with EGFR mutation": [[36, "compare-the-individuals-with-egfr-mutation"]], "Compare the individuals with monoallelic and biallelic mutations": [[36, "compare-the-individuals-with-monoallelic-and-biallelic-mutations"]], "Complex conditions": [[45, "complex-conditions"]], "Configure a cohort creator": [[34, "configure-a-cohort-creator"]], "Configure analysis": [[25, "configure-analysis"], [26, "configure-analysis"], [27, "configure-analysis"], [28, "configure-analysis"]], "Contents:": [[24, null], [33, null], [39, null], [41, null], [42, null]], "Create a cohort from GA4GH phenopackets": [[34, "create-a-cohort-from-ga4gh-phenopackets"]], "Custom analysis": [[26, "custom-analysis"]], "De Vries Score": [[37, null]], "Default analysis": [[26, "default-analysis"]], "Developmental delay": [[37, "developmental-delay"]], "Distribution of variants across protein domains": [[30, "distribution-of-variants-across-protein-domains"]], "Enter features manually": [[34, "enter-features-manually"]], "Example": [[34, "example"], [34, "id4"], [40, "example"], [44, "example"], [44, "id5"], [44, "id6"]], "Example analysis": [[25, "example-analysis"], [26, "example-analysis"], [27, "example-analysis"], [28, "example-analysis"]], "Examples": [[36, "examples"]], "Exploration": [[30, "exploration"]], "Explore cohort": [[23, "explore-cohort"]], "Facial dysmorphic features": [[37, "facial-dysmorphic-features"]], "Feedback": [[21, "feedback"]], "Fetch data from UniProt REST API": [[34, "fetch-data-from-uniprot-rest-api"]], "Fetch protein data": [[34, "fetch-protein-data"]], "Fetch transcript coordinates from Variant Validator REST API": [[34, "fetch-transcript-coordinates-from-variant-validator-rest-api"]], "Final analysis": [[25, "final-analysis"], [27, "final-analysis"], [28, "final-analysis"]], "Final score": [[37, "final-score"]], "Fisher exact test (FET)": [[26, "fisher-exact-test-fet"]], "GPSEA": [[21, null]], "Gallery": [[41, "gallery"]], "General HPO terms": [[31, null]], "Genotype Predicates": [[39, null]], "Genotype phenotype associations": [[26, "genotype-phenotype-associations"]], "Genotype predicate": [[25, "genotype-predicate"], [26, "genotype-predicate"], [27, "genotype-predicate"], [28, "genotype-predicate"]], "Genotype-Phenotype Correlations in Autosomal Recessive Diseases": [[29, null]], "Get the transcript data": [[34, "get-the-transcript-data"]], "Glossary": [[32, null]], "Group by allele count": [[36, null]], "Group by diagnosis": [[38, null]], "Group by sex": [[43, null]], "Group by variant category": [[44, null]], "HMF01 - Skip terms that occur very rarely": [[35, "hmf01-skip-terms-that-occur-very-rarely"]], "HMF02 - Skip terms if no genotype group has more than one count": [[35, "hmf02-skip-terms-if-no-genotype-group-has-more-than-one-count"]], "HMF03 - Skip terms if all counts are identical to counts for a child term": [[35, "hmf03-skip-terms-if-all-counts-are-identical-to-counts-for-a-child-term"]], "HMF05 - Skip term if one of the genotype groups has neither observed nor excluded observations": [[35, "hmf05-skip-term-if-one-of-the-genotype-groups-has-neither-observed-nor-excluded-observations"]], "HMF06 - Skip term if underpowered for 2x2 or 2x3 analysis": [[35, "hmf06-skip-term-if-underpowered-for-2x2-or-2x3-analysis"]], "HMF07 - Skipping terms that are not descendents of Phenotypic abnormality": [[35, "hmf07-skipping-terms-that-are-not-descendents-of-phenotypic-abnormality"]], "HMF08 - Skipping \u201cgeneral\u201d level terms": [[35, "hmf08-skipping-general-level-terms"]], "HMF09 - Skipping terms that are rare on the cohort level": [[35, "hmf09-skipping-terms-that-are-rare-on-the-cohort-level"]], "HPO MT filter strategy": [[35, "hpo-mt-filter-strategy"]], "HPO predicate": [[40, null]], "Implementation in GPSEA": [[35, "implementation-in-gpsea"]], "Input data": [[34, null]], "Installation": [[22, null]], "Interactive exploration": [[30, "interactive-exploration"]], "Inverting conditions": [[45, "inverting-conditions"]], "Kaplan-Meier curves": [[28, "kaplan-meier-curves"]], "Latest release": [[22, "latest-release"]], "Length of the reference allele": [[32, "length-of-the-reference-allele"]], "Literature": [[21, "literature"]], "Load HPO": [[23, "load-hpo"], [27, "load-hpo"]], "Load cohort": [[25, "load-cohort"], [26, "load-cohort"], [27, "load-cohort"], [28, "load-cohort"], [45, "load-cohort"]], "Load phenopackets": [[34, "load-phenopackets"]], "MT filters: Choosing which terms to test": [[35, "mt-filters-choosing-which-terms-to-test"]], "Mann-Whitney U Test": [[27, "mann-whitney-u-test"]], "Monoallelic predicate": [[44, "monoallelic-predicate"]], "Monoallelic predicate genotype groups": [[44, "id7"]], "Multiple-testing correction": [[35, null]], "Multiple-testing correction procedures": [[35, "multiple-testing-correction-procedures"]], "Need more?": [[41, "need-more"]], "Non-facial dysmorphism and congenital abnormalities": [[37, "non-facial-dysmorphism-and-congenital-abnormalities"]], "Parse UniProt JSON dump": [[34, "parse-uniprot-json-dump"]], "Partitions": [[44, "partitions"]], "Persist the cohort for later": [[34, "persist-the-cohort-for-later"]], "Phenotype Predicates": [[42, null]], "Phenotype predicates": [[26, "phenotype-predicates"]], "Phenotype score": [[25, "phenotype-score"], [27, "phenotype-score"]], "Plot distribution of cohort variants on the protein": [[34, "plot-distribution-of-cohort-variants-on-the-protein"]], "Plot distribution of variants with respect to the protein sequence": [[23, "plot-distribution-of-variants-with-respect-to-the-protein-sequence"], [30, "plot-distribution-of-variants-with-respect-to-the-protein-sequence"]], "Postnatal growth abnormalities": [[37, "postnatal-growth-abnormalities"]], "Power": [[30, "power"]], "Predicates": [[41, null]], "Predicates for all cohort phenotypes": [[40, "predicates-for-all-cohort-phenotypes"]], "Prenatal-onset growth retardation": [[37, "prenatal-onset-growth-retardation"]], "Prepare cohort": [[23, "prepare-cohort"]], "Prepare genotype and phenotype predicates": [[23, "prepare-genotype-and-phenotype-predicates"]], "Provide the transcript coordinates manually": [[34, "provide-the-transcript-coordinates-manually"]], "Quality control": [[34, "quality-control"]], "Raw data": [[28, "raw-data"]], "Run tests": [[22, "run-tests"]], "Show cohort summary": [[23, "show-cohort-summary"]], "Showcase transcript data": [[34, "showcase-transcript-data"]], "Specify terms strategy": [[35, "specify-terms-strategy"]], "Stable release": [[22, "stable-release"]], "Standardize genotype and phenotype data": [[34, "standardize-genotype-and-phenotype-data"]], "Statistical analyses": [[24, null]], "Statistical analysis": [[26, "statistical-analysis"]], "Statistical test": [[25, "statistical-test"], [27, "statistical-test"], [28, "statistical-test"]], "Submodules": [[0, "submodules"]], "Subpackages": [[0, "subpackages"], [1, "subpackages"], [3, "subpackages"], [5, "subpackages"], [8, "subpackages"], [10, "subpackages"], [15, "subpackages"]], "Summarize all variant alleles": [[23, "summarize-all-variant-alleles"]], "Supports shape": [[4, "supports-shape"]], "Survival analysis": [[28, null]], "Survival endpoint": [[28, "survival-endpoint"]], "TBX5 frameshift vs missense": [[23, "id5"]], "TBX5 frameshift vs rest": [[26, "id1"]], "Test all terms": [[35, "test-all-terms"]], "The analysis": [[23, "the-analysis"]], "The sections of the score": [[37, "the-sections-of-the-score"]], "True path rule": [[32, "true-path-rule"]], "Tutorial": [[23, null], [29, "tutorial"]], "Types of statistical test": [[30, "types-of-statistical-test"]], "User guide": [[33, null]], "Using the De Vries scorer in code": [[37, "using-the-de-vries-scorer-in-code"]], "Variant Predicates": [[45, null]], "gpsea package": [[0, null]], "gpsea.analysis package": [[1, null]], "gpsea.analysis.mtc_filter package": [[2, null]], "gpsea.analysis.pcats package": [[3, null]], "gpsea.analysis.pcats.stats package": [[4, null]], "gpsea.analysis.predicate package": [[5, null]], "gpsea.analysis.predicate.genotype package": [[6, null]], "gpsea.analysis.predicate.phenotype package": [[7, null]], "gpsea.analysis.pscore package": [[8, null]], "gpsea.analysis.pscore.stats package": [[9, null]], "gpsea.analysis.temporal package": [[10, null]], "gpsea.analysis.temporal.endpoint package": [[11, null]], "gpsea.analysis.temporal.stats package": [[12, null]], "gpsea.config module": [[13, null]], "gpsea.io module": [[14, null]], "gpsea.model package": [[15, null]], "gpsea.model.genome package": [[16, null]], "gpsea.preprocessing package": [[17, null]], "gpsea.util module": [[18, null]], "gpsea.view package": [[19, null]], "missing_implies_phenotype_excluded": [[40, "missing-implies-phenotype-excluded"]]}, "docnames": ["apidocs/gpsea", "apidocs/gpsea.analysis", "apidocs/gpsea.analysis.mtc_filter", "apidocs/gpsea.analysis.pcats", "apidocs/gpsea.analysis.pcats.stats", "apidocs/gpsea.analysis.predicate", "apidocs/gpsea.analysis.predicate.genotype", "apidocs/gpsea.analysis.predicate.phenotype", "apidocs/gpsea.analysis.pscore", "apidocs/gpsea.analysis.pscore.stats", "apidocs/gpsea.analysis.temporal", "apidocs/gpsea.analysis.temporal.endpoint", "apidocs/gpsea.analysis.temporal.stats", "apidocs/gpsea.config", "apidocs/gpsea.io", "apidocs/gpsea.model", "apidocs/gpsea.model.genome", "apidocs/gpsea.preprocessing", "apidocs/gpsea.util", "apidocs/gpsea.view", "apidocs/modules", "index", "installation", "tutorial", "user-guide/analyses/index", "user-guide/analyses/measurements", "user-guide/analyses/phenotype-groups", "user-guide/analyses/phenotype-scores", "user-guide/analyses/survival", "user-guide/autosomal_recessive", "user-guide/exploratory", "user-guide/general_hpo_terms", "user-guide/glossary", "user-guide/index", "user-guide/input-data", "user-guide/mtc", "user-guide/predicates/allele_count", "user-guide/predicates/devries", "user-guide/predicates/diagnosis", "user-guide/predicates/genotype_predicates", "user-guide/predicates/hpo_predicate", "user-guide/predicates/index", "user-guide/predicates/phenotype_predicates", "user-guide/predicates/sex", "user-guide/predicates/variant_category", "user-guide/predicates/variant_predicates"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["apidocs/gpsea.rst", "apidocs/gpsea.analysis.rst", "apidocs/gpsea.analysis.mtc_filter.rst", "apidocs/gpsea.analysis.pcats.rst", "apidocs/gpsea.analysis.pcats.stats.rst", "apidocs/gpsea.analysis.predicate.rst", "apidocs/gpsea.analysis.predicate.genotype.rst", "apidocs/gpsea.analysis.predicate.phenotype.rst", "apidocs/gpsea.analysis.pscore.rst", "apidocs/gpsea.analysis.pscore.stats.rst", "apidocs/gpsea.analysis.temporal.rst", "apidocs/gpsea.analysis.temporal.endpoint.rst", "apidocs/gpsea.analysis.temporal.stats.rst", "apidocs/gpsea.config.rst", "apidocs/gpsea.io.rst", "apidocs/gpsea.model.rst", "apidocs/gpsea.model.genome.rst", "apidocs/gpsea.preprocessing.rst", "apidocs/gpsea.util.rst", "apidocs/gpsea.view.rst", "apidocs/modules.rst", "index.rst", "installation.rst", "tutorial.rst", "user-guide/analyses/index.rst", "user-guide/analyses/measurements.rst", "user-guide/analyses/phenotype-groups.rst", "user-guide/analyses/phenotype-scores.rst", "user-guide/analyses/survival.rst", "user-guide/autosomal_recessive.rst", "user-guide/exploratory.rst", "user-guide/general_hpo_terms.rst", "user-guide/glossary.rst", "user-guide/index.rst", "user-guide/input-data.rst", "user-guide/mtc.rst", "user-guide/predicates/allele_count.rst", "user-guide/predicates/devries.rst", "user-guide/predicates/diagnosis.rst", "user-guide/predicates/genotype_predicates.rst", "user-guide/predicates/hpo_predicate.rst", "user-guide/predicates/index.rst", "user-guide/predicates/phenotype_predicates.rst", "user-guide/predicates/sex.rst", "user-guide/predicates/variant_category.rst", "user-guide/predicates/variant_predicates.rst"], "indexentries": {"age (class in gpsea.model)": [[15, "gpsea.model.Age", false]], "age (gpsea.model.patient property)": [[15, "gpsea.model.Patient.age", false]], "age_of_death (gpsea.model.vitalstatus attribute)": [[15, "gpsea.model.VitalStatus.age_of_death", false]], "alive (gpsea.model.status attribute)": [[15, "gpsea.model.Status.ALIVE", false]], "all() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.all", false]], "all_counts (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.all_counts", false]], "all_counts (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.all_counts", false]], "all_diseases() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_diseases", false]], "all_measurements() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_measurements", false]], "all_patients (gpsea.model.cohort property)": [[15, "gpsea.model.Cohort.all_patients", false]], "all_phenotypes() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_phenotypes", false]], "all_transcript_ids (gpsea.model.cohort property)": [[15, "gpsea.model.Cohort.all_transcript_ids", false]], "all_variant_infos() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_variant_infos", false]], "all_variants() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_variants", false]], "allele_count() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.allele_count", false]], "allelecounter (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.AlleleCounter", false]], "alt (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.alt", false]], "analysisresult (class in gpsea.analysis)": [[1, "gpsea.analysis.AnalysisResult", false]], "annotate() (gpsea.preprocessing.defaultimprecisesvfunctionalannotator method)": [[17, "gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.functionalannotator method)": [[17, "gpsea.preprocessing.FunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.imprecisesvfunctionalannotator method)": [[17, "gpsea.preprocessing.ImpreciseSvFunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.protcachingmetadataservice method)": [[17, "gpsea.preprocessing.ProtCachingMetadataService.annotate", false]], "annotate() (gpsea.preprocessing.proteinmetadataservice method)": [[17, "gpsea.preprocessing.ProteinMetadataService.annotate", false]], "annotate() (gpsea.preprocessing.uniprotproteinmetadataservice method)": [[17, "gpsea.preprocessing.UniprotProteinMetadataService.annotate", false]], "annotate() (gpsea.preprocessing.varcachingfunctionalannotator method)": [[17, "gpsea.preprocessing.VarCachingFunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.vepfunctionalannotator method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.annotate", false]], "any() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.any", false]], "apply_predicates_on_patients() (in module gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.apply_predicates_on_patients", false]], "biallelic_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.biallelic_predicate", false]], "birth() (gpsea.model.age static method)": [[15, "gpsea.model.Age.birth", false]], "cache_env (in module gpsea.config)": [[13, "gpsea.config.CACHE_ENV", false]], "cds_end (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.cds_end", false]], "cds_start (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.cds_start", false]], "change_length (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.change_length", false]], "change_length() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.change_length", false]], "chrom (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.chrom", false]], "code (gpsea.analysis.mtc_filter.phenotypemtcissue attribute)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcIssue.code", false]], "code (gpsea.model.genotype property)": [[15, "gpsea.model.Genotype.code", false]], "coding_sequence_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.CODING_SEQUENCE_VARIANT", false]], "cohort (class in gpsea.model)": [[15, "gpsea.model.Cohort", false]], "cohortcreator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.CohortCreator", false]], "cohortvariantviewer (class in gpsea.view)": [[19, "gpsea.view.CohortVariantViewer", false]], "cohortviewer (class in gpsea.view)": [[19, "gpsea.view.CohortViewer", false]], "coiled_coil (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.COILED_COIL", false]], "compare_genotype_vs_phenotype_score() (gpsea.analysis.pscore.phenotypescoreanalysis method)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysis.compare_genotype_vs_phenotype_score", false]], "compare_genotype_vs_phenotypes() (gpsea.analysis.pcats.multiphenotypeanalysis method)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysis.compare_genotype_vs_phenotypes", false]], "compare_genotype_vs_survival() (gpsea.analysis.temporal.survivalanalysis method)": [[10, "gpsea.analysis.temporal.SurvivalAnalysis.compare_genotype_vs_survival", false]], "complete_records() (gpsea.analysis.monophenotypeanalysisresult method)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.complete_records", false]], "compositional_bias (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.COMPOSITIONAL_BIAS", false]], "compute_pval() (gpsea.analysis.pcats.stats.countstatistic method)": [[4, "gpsea.analysis.pcats.stats.CountStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.pcats.stats.fisherexacttest method)": [[4, "gpsea.analysis.pcats.stats.FisherExactTest.compute_pval", false]], "compute_pval() (gpsea.analysis.pscore.stats.mannwhitneystatistic method)": [[9, "gpsea.analysis.pscore.stats.MannWhitneyStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.pscore.stats.phenotypescorestatistic method)": [[9, "gpsea.analysis.pscore.stats.PhenotypeScoreStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.pscore.stats.tteststatistic method)": [[9, "gpsea.analysis.pscore.stats.TTestStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.temporal.stats.logranktest method)": [[12, "gpsea.analysis.temporal.stats.LogRankTest.compute_pval", false]], "compute_pval() (gpsea.analysis.temporal.stats.survivalstatistic method)": [[12, "gpsea.analysis.temporal.stats.SurvivalStatistic.compute_pval", false]], "compute_survival() (gpsea.analysis.temporal.endpoint method)": [[10, "gpsea.analysis.temporal.Endpoint.compute_survival", false]], "configure_caching_cohort_creator() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_caching_cohort_creator", false]], "configure_cohort_creator() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_cohort_creator", false]], "configure_default_protein_metadata_service() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_default_protein_metadata_service", false]], "configure_hpo_term_analysis() (in module gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.configure_hpo_term_analysis", false]], "configure_protein_metadata_service() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_protein_metadata_service", false]], "contains() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.contains", false]], "contains() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.contains", false]], "contains_pos() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.contains_pos", false]], "contig (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Contig", false]], "contig (gpsea.model.genome.genomicregion property)": [[16, "gpsea.model.genome.GenomicRegion.contig", false]], "contig_by_name() (gpsea.model.genome.genomebuild method)": [[16, "gpsea.model.genome.GenomeBuild.contig_by_name", false]], "contigs (gpsea.model.genome.genomebuild property)": [[16, "gpsea.model.genome.GenomeBuild.contigs", false]], "corrected_pvals (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.corrected_pvals", false]], "corrected_pvals (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.corrected_pvals", false]], "count() (gpsea.analysis.predicate.genotype.allelecounter method)": [[6, "gpsea.analysis.predicate.genotype.AlleleCounter.count", false]], "count_alive() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_alive", false]], "count_deceased() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_deceased", false]], "count_distinct_diseases() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_distinct_diseases", false]], "count_distinct_hpo_terms() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_distinct_hpo_terms", false]], "count_distinct_measurements() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_distinct_measurements", false]], "count_females() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_females", false]], "count_males() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_males", false]], "count_unique_diseases() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.count_unique_diseases", false]], "count_unique_measurements() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.count_unique_measurements", false]], "count_unique_phenotypes() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.count_unique_phenotypes", false]], "count_unknown_sex() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_unknown_sex", false]], "count_unknown_vital_status() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_unknown_vital_status", false]], "count_with_age_of_last_encounter() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_with_age_of_last_encounter", false]], "count_with_disease_onset() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_with_disease_onset", false]], "countingphenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer", false]], "countstatistic (class in gpsea.analysis.pcats.stats)": [[4, "gpsea.analysis.pcats.stats.CountStatistic", false]], "create() (gpsea.model.proteinfeature static method)": [[15, "gpsea.model.ProteinFeature.create", false]], "create_variant_from_scratch() (gpsea.model.variant static method)": [[15, "gpsea.model.Variant.create_variant_from_scratch", false]], "curie (gpsea.model.varianteffect property)": [[15, "gpsea.model.VariantEffect.curie", false]], "data (gpsea.analysis.monophenotypeanalysisresult property)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.data", false]], "data_columns (gpsea.analysis.monophenotypeanalysisresult attribute)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.DATA_COLUMNS", false]], "days (gpsea.model.age property)": [[15, "gpsea.model.Age.days", false]], "days_in_month (gpsea.model.age attribute)": [[15, "gpsea.model.Age.DAYS_IN_MONTH", false]], "days_in_week (gpsea.model.age attribute)": [[15, "gpsea.model.Age.DAYS_IN_WEEK", false]], "days_in_year (gpsea.model.age attribute)": [[15, "gpsea.model.Age.DAYS_IN_YEAR", false]], "death() (in module gpsea.analysis.temporal.endpoint)": [[11, "gpsea.analysis.temporal.endpoint.death", false]], "deceased (gpsea.model.status attribute)": [[15, "gpsea.model.Status.DECEASED", false]], "default() (gpsea.io.gpseajsonencoder method)": [[14, "gpsea.io.GpseaJSONEncoder.default", false]], "default_cache_path (in module gpsea.config)": [[13, "gpsea.config.DEFAULT_CACHE_PATH", false]], "default_filter() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter", false]], "default_parser() (gpsea.preprocessing.phenopacketontologytermonsetparser static method)": [[17, "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser.default_parser", false]], "defaultimprecisesvfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator", false]], "del (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.DEL", false]], "description (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.description", false]], "description (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.description", false]], "description (gpsea.analysis.pscore.countingphenotypescorer property)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.description", false]], "description (gpsea.analysis.pscore.devriesphenotypescorer property)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.description", false]], "description (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.description", false]], "devriesphenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer", false]], "diagnosis_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.diagnosis_predicate", false]], "disease (class in gpsea.model)": [[15, "gpsea.model.Disease", false]], "disease_by_id() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.disease_by_id", false]], "disease_onset() (in module gpsea.analysis.temporal.endpoint)": [[11, "gpsea.analysis.temporal.endpoint.disease_onset", false]], "diseaseanalysis (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.DiseaseAnalysis", false]], "diseasepresencepredicate (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate", false]], "diseases (gpsea.model.patient property)": [[15, "gpsea.model.Patient.diseases", false]], "diseaseviewer (class in gpsea.view)": [[19, "gpsea.view.DiseaseViewer", false]], "distance_to() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.distance_to", false]], "distance_to() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.distance_to", false]], "domain (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.DOMAIN", false]], "domains() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.domains", false]], "downstream_gene_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.DOWNSTREAM_GENE_VARIANT", false]], "draw_fig() (gpsea.view.proteinvisualizer method)": [[19, "gpsea.view.ProteinVisualizer.draw_fig", false]], "draw_protein_diagram() (gpsea.view.proteinvisualizer method)": [[19, "gpsea.view.ProteinVisualizer.draw_protein_diagram", false]], "draw_variants() (gpsea.view.varianttranscriptvisualizer method)": [[19, "gpsea.view.VariantTranscriptVisualizer.draw_variants", false]], "dup (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.DUP", false]], "empty() (gpsea.model.genotypes static method)": [[15, "gpsea.model.Genotypes.empty", false]], "end (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.end", false]], "end (gpsea.model.genome.region property)": [[16, "gpsea.model.genome.Region.end", false]], "end (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.end", false]], "end_on_strand() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.end_on_strand", false]], "endpoint (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.Endpoint", false]], "endpoint (gpsea.analysis.temporal.survivalanalysisresult property)": [[10, "gpsea.analysis.temporal.SurvivalAnalysisResult.endpoint", false]], "excluded_diseases() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.excluded_diseases", false]], "excluded_phenotypes() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.excluded_phenotypes", false]], "exon() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.exon", false]], "exons (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.exons", false]], "fail() (gpsea.analysis.mtc_filter.phenotypemtcresult static method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.fail", false]], "feature_elongation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FEATURE_ELONGATION", false]], "feature_truncation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FEATURE_TRUNCATION", false]], "feature_type (gpsea.model.proteinfeature property)": [[15, "gpsea.model.ProteinFeature.feature_type", false]], "featureinfo (class in gpsea.model)": [[15, "gpsea.model.FeatureInfo", false]], "featuretype (class in gpsea.model)": [[15, "gpsea.model.FeatureType", false]], "female (gpsea.model.sex attribute)": [[15, "gpsea.model.Sex.FEMALE", false]], "fetch() (gpsea.preprocessing.transcriptcoordinateservice method)": [[17, "gpsea.preprocessing.TranscriptCoordinateService.fetch", false]], "fetch() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.fetch", false]], "fetch_for_gene() (gpsea.preprocessing.genecoordinateservice method)": [[17, "gpsea.preprocessing.GeneCoordinateService.fetch_for_gene", false]], "fetch_for_gene() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.fetch_for_gene", false]], "fetch_response() (gpsea.preprocessing.vepfunctionalannotator method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.fetch_response", false]], "filter() (gpsea.analysis.mtc_filter.hpomtcfilter method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.filter", false]], "filter() (gpsea.analysis.mtc_filter.phenotypemtcfilter method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter", false]], "filter() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter", false]], "filter() (gpsea.analysis.mtc_filter.usealltermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter", false]], "filter_method_name() (gpsea.analysis.mtc_filter.hpomtcfilter method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.filter_method_name", false]], "filter_method_name() (gpsea.analysis.mtc_filter.phenotypemtcfilter method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter_method_name", false]], "filter_method_name() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter_method_name", false]], "filter_method_name() (gpsea.analysis.mtc_filter.usealltermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter_method_name", false]], "find_coordinates() (gpsea.preprocessing.phenopacketvariantcoordinatefinder method)": [[17, "gpsea.preprocessing.PhenopacketVariantCoordinateFinder.find_coordinates", false]], "find_coordinates() (gpsea.preprocessing.variantcoordinatefinder method)": [[17, "gpsea.preprocessing.VariantCoordinateFinder.find_coordinates", false]], "find_coordinates() (gpsea.preprocessing.vvhgvsvariantcoordinatefinder method)": [[17, "gpsea.preprocessing.VVHgvsVariantCoordinateFinder.find_coordinates", false]], "fisherexacttest (class in gpsea.analysis.pcats.stats)": [[4, "gpsea.analysis.pcats.stats.FisherExactTest", false]], "five_prime_utr_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FIVE_PRIME_UTR_VARIANT", false]], "for_sample() (gpsea.model.genotypes method)": [[15, "gpsea.model.Genotypes.for_sample", false]], "format_as_string() (gpsea.view.formatter method)": [[19, "gpsea.view.Formatter.format_as_string", false]], "format_as_string() (gpsea.view.variantformatter method)": [[19, "gpsea.view.VariantFormatter.format_as_string", false]], "format_coordinates_for_vep_query() (gpsea.preprocessing.vepfunctionalannotator static method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.format_coordinates_for_vep_query", false]], "formatter (class in gpsea.view)": [[19, "gpsea.view.Formatter", false]], "frameshift_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FRAMESHIFT_VARIANT", false]], "from_feature_frame() (gpsea.model.proteinmetadata static method)": [[15, "gpsea.model.ProteinMetadata.from_feature_frame", false]], "from_iso8601_period() (gpsea.model.age static method)": [[15, "gpsea.model.Age.from_iso8601_period", false]], "from_mapping() (gpsea.model.genotypes static method)": [[15, "gpsea.model.Genotypes.from_mapping", false]], "from_measurement_id() (gpsea.analysis.pscore.measurementphenotypescorer static method)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.from_measurement_id", false]], "from_patients() (gpsea.model.cohort static method)": [[15, "gpsea.model.Cohort.from_patients", false]], "from_query_curies() (gpsea.analysis.pscore.countingphenotypescorer static method)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.from_query_curies", false]], "from_raw_parts() (gpsea.model.disease static method)": [[15, "gpsea.model.Disease.from_raw_parts", false]], "from_raw_parts() (gpsea.model.patient static method)": [[15, "gpsea.model.Patient.from_raw_parts", false]], "from_raw_parts() (gpsea.model.phenotype static method)": [[15, "gpsea.model.Phenotype.from_raw_parts", false]], "from_string() (gpsea.model.featuretype static method)": [[15, "gpsea.model.FeatureType.from_string", false]], "from_term() (gpsea.model.phenotype static method)": [[15, "gpsea.model.Phenotype.from_term", false]], "from_uniprot_json() (gpsea.model.proteinmetadata static method)": [[15, "gpsea.model.ProteinMetadata.from_uniprot_json", false]], "from_vcf_literal() (gpsea.model.variantcoordinates static method)": [[15, "gpsea.model.VariantCoordinates.from_vcf_literal", false]], "from_vcf_symbolic() (gpsea.model.variantcoordinates static method)": [[15, "gpsea.model.VariantCoordinates.from_vcf_symbolic", false]], "functionalannotationaware (class in gpsea.model)": [[15, "gpsea.model.FunctionalAnnotationAware", false]], "functionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.FunctionalAnnotator", false]], "genbank_acc (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.genbank_acc", false]], "gene() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.gene", false]], "gene_id (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.gene_id", false]], "gene_id (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.gene_id", false]], "gene_id (gpsea.model.transcriptinfoaware property)": [[15, "gpsea.model.TranscriptInfoAware.gene_id", false]], "gene_symbol (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.gene_symbol", false]], "genecoordinateservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.GeneCoordinateService", false]], "genome_build_id (gpsea.model.genome.genomebuild property)": [[16, "gpsea.model.genome.GenomeBuild.genome_build_id", false]], "genomebuild (class in gpsea.model.genome)": [[16, "gpsea.model.genome.GenomeBuild", false]], "genomebuildidentifier (class in gpsea.model.genome)": [[16, "gpsea.model.genome.GenomeBuildIdentifier", false]], "genomicregion (class in gpsea.model.genome)": [[16, "gpsea.model.genome.GenomicRegion", false]], "genotype (class in gpsea.model)": [[15, "gpsea.model.Genotype", false]], "genotype_for_sample() (gpsea.model.genotyped method)": [[15, "gpsea.model.Genotyped.genotype_for_sample", false]], "genotyped (class in gpsea.model)": [[15, "gpsea.model.Genotyped", false]], "genotypepolypredicate (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.GenotypePolyPredicate", false]], "genotypes (class in gpsea.model)": [[15, "gpsea.model.Genotypes", false]], "genotypes (gpsea.model.genotyped property)": [[15, "gpsea.model.Genotyped.genotypes", false]], "genotypes (gpsea.model.variant property)": [[15, "gpsea.model.Variant.genotypes", false]], "gestational (gpsea.model.timeline attribute)": [[15, "gpsea.model.Timeline.GESTATIONAL", false]], "gestational() (gpsea.model.age static method)": [[15, "gpsea.model.Age.gestational", false]], "gestational_days() (gpsea.model.age static method)": [[15, "gpsea.model.Age.gestational_days", false]], "get_annotations() (gpsea.preprocessing.proteinannotationcache method)": [[17, "gpsea.preprocessing.ProteinAnnotationCache.get_annotations", false]], "get_annotations() (gpsea.preprocessing.variantannotationcache method)": [[17, "gpsea.preprocessing.VariantAnnotationCache.get_annotations", false]], "get_cache_dir_path() (in module gpsea.config)": [[13, "gpsea.config.get_cache_dir_path", false]], "get_categories() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_categories", false]], "get_categorizations() (gpsea.analysis.predicate.phenotype.diseasepresencepredicate method)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.get_categorizations", false]], "get_categorizations() (gpsea.analysis.predicate.phenotype.hpopredicate method)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.get_categorizations", false]], "get_categorizations() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_categorizations", false]], "get_category() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_category", false]], "get_category_name() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_category_name", false]], "get_cds_regions() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_cds_regions", false]], "get_coding_base_count() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_coding_base_count", false]], "get_codon_count() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_codon_count", false]], "get_excluded_count() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.get_excluded_count", false]], "get_features_variant_overlaps() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.get_features_variant_overlaps", false]], "get_five_prime_utrs() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_five_prime_utrs", false]], "get_hgvs_cdna_by_tx_id() (gpsea.model.functionalannotationaware method)": [[15, "gpsea.model.FunctionalAnnotationAware.get_hgvs_cdna_by_tx_id", false]], "get_maximum_group_observed_hpo_frequency() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.get_maximum_group_observed_HPO_frequency", false]], "get_number_of_observed_hpo_observations() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.get_number_of_observed_hpo_observations", false]], "get_patient_ids() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.get_patient_ids", false]], "get_preferred_tx_annotation() (gpsea.model.functionalannotationaware method)": [[15, "gpsea.model.FunctionalAnnotationAware.get_preferred_tx_annotation", false]], "get_question() (gpsea.analysis.predicate.genotype.allelecounter method)": [[6, "gpsea.analysis.predicate.genotype.AlleleCounter.get_question", false]], "get_question() (gpsea.analysis.predicate.genotype.variantpredicate method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicate.get_question", false]], "get_response() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.get_response", false]], "get_three_prime_utrs() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_three_prime_utrs", false]], "get_tx_anno_by_tx_id() (gpsea.model.functionalannotationaware method)": [[15, "gpsea.model.FunctionalAnnotationAware.get_tx_anno_by_tx_id", false]], "get_variant_by_key() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.get_variant_by_key", false]], "gpsea": [[0, "module-gpsea", false]], "gpsea.analysis": [[1, "module-gpsea.analysis", false]], "gpsea.analysis.mtc_filter": [[2, "module-gpsea.analysis.mtc_filter", false]], "gpsea.analysis.pcats": [[3, "module-gpsea.analysis.pcats", false]], "gpsea.analysis.pcats.stats": [[4, "module-gpsea.analysis.pcats.stats", false]], "gpsea.analysis.predicate": [[5, "module-gpsea.analysis.predicate", false]], "gpsea.analysis.predicate.genotype": [[6, "module-gpsea.analysis.predicate.genotype", false]], "gpsea.analysis.predicate.phenotype": [[7, "module-gpsea.analysis.predicate.phenotype", false]], "gpsea.analysis.pscore": [[8, "module-gpsea.analysis.pscore", false]], "gpsea.analysis.pscore.stats": [[9, "module-gpsea.analysis.pscore.stats", false]], "gpsea.analysis.temporal": [[10, "module-gpsea.analysis.temporal", false]], "gpsea.analysis.temporal.endpoint": [[11, "module-gpsea.analysis.temporal.endpoint", false]], "gpsea.analysis.temporal.stats": [[12, "module-gpsea.analysis.temporal.stats", false]], "gpsea.config": [[13, "module-gpsea.config", false]], "gpsea.io": [[14, "module-gpsea.io", false]], "gpsea.model": [[15, "module-gpsea.model", false]], "gpsea.model.genome": [[16, "module-gpsea.model.genome", false]], "gpsea.preprocessing": [[17, "module-gpsea.preprocessing", false]], "gpsea.util": [[18, "module-gpsea.util", false]], "gpsea.view": [[19, "module-gpsea.view", false]], "gpseajsondecoder (class in gpsea.io)": [[14, "gpsea.io.GpseaJSONDecoder", false]], "gpseajsonencoder (class in gpsea.io)": [[14, "gpsea.io.GpseaJSONEncoder", false]], "gpseareport (class in gpsea.view)": [[19, "gpsea.view.GpseaReport", false]], "group_labels (gpsea.analysis.predicate.polypredicate property)": [[5, "gpsea.analysis.predicate.PolyPredicate.group_labels", false]], "gt_col (gpsea.analysis.monophenotypeanalysisresult attribute)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.GT_COL", false]], "gt_predicate (gpsea.analysis.analysisresult property)": [[1, "gpsea.analysis.AnalysisResult.gt_predicate", false]], "has_sv_info() (gpsea.model.variantinfo method)": [[15, "gpsea.model.VariantInfo.has_sv_info", false]], "has_variant_coordinates() (gpsea.model.variantinfo method)": [[15, "gpsea.model.VariantInfo.has_variant_coordinates", false]], "hemizygous (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HEMIZYGOUS", false]], "heterozygous (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HETEROZYGOUS", false]], "hgvs_cdna (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.hgvs_cdna", false]], "hgvsp (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.hgvsp", false]], "homozygous_alternate (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HOMOZYGOUS_ALTERNATE", false]], "homozygous_reference (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HOMOZYGOUS_REFERENCE", false]], "hpo_onset() (in module gpsea.analysis.temporal.endpoint)": [[11, "gpsea.analysis.temporal.endpoint.hpo_onset", false]], "hpomtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter", false]], "hpopredicate (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate", false]], "hpotermanalysis (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.HpoTermAnalysis", false]], "hpotermanalysisresult (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult", false]], "identifier (gpsea.model.disease property)": [[15, "gpsea.model.Disease.identifier", false]], "identifier (gpsea.model.genome.genomebuild property)": [[16, "gpsea.model.genome.GenomeBuild.identifier", false]], "identifier (gpsea.model.genome.genomebuildidentifier property)": [[16, "gpsea.model.genome.GenomeBuildIdentifier.identifier", false]], "identifier (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.identifier", false]], "identifier (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.identifier", false]], "identifier (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.identifier", false]], "imprecisesvfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ImpreciseSvFunctionalAnnotator", false]], "imprecisesvinfo (class in gpsea.model)": [[15, "gpsea.model.ImpreciseSvInfo", false]], "incomplete_terminal_codon_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INCOMPLETE_TERMINAL_CODON_VARIANT", false]], "info (gpsea.model.proteinfeature property)": [[15, "gpsea.model.ProteinFeature.info", false]], "inframe_deletion (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INFRAME_DELETION", false]], "inframe_insertion (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INFRAME_INSERTION", false]], "ins (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.INS", false]], "intergenic_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INTERGENIC_VARIANT", false]], "intron_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INTRON_VARIANT", false]], "inv (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.INV", false]], "is_alive (gpsea.model.vitalstatus property)": [[15, "gpsea.model.VitalStatus.is_alive", false]], "is_censored (gpsea.analysis.temporal.survival attribute)": [[10, "gpsea.analysis.temporal.Survival.is_censored", false]], "is_coding() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.is_coding", false]], "is_deceased (gpsea.model.vitalstatus property)": [[15, "gpsea.model.VitalStatus.is_deceased", false]], "is_empty() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.is_empty", false]], "is_female() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_female", false]], "is_filtered_out() (gpsea.analysis.mtc_filter.phenotypemtcresult method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out", false]], "is_gestational (gpsea.model.age property)": [[15, "gpsea.model.Age.is_gestational", false]], "is_large_imprecise_sv() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.is_large_imprecise_sv", false]], "is_male() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_male", false]], "is_negative() (gpsea.model.genome.strand method)": [[16, "gpsea.model.genome.Strand.is_negative", false]], "is_observed (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.is_observed", false]], "is_ok() (gpsea.preprocessing.preprocessingvalidationresult method)": [[17, "gpsea.preprocessing.PreprocessingValidationResult.is_ok", false]], "is_passed() (gpsea.analysis.mtc_filter.phenotypemtcresult method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_passed", false]], "is_positive() (gpsea.model.genome.strand method)": [[16, "gpsea.model.genome.Strand.is_positive", false]], "is_postnatal (gpsea.model.age property)": [[15, "gpsea.model.Age.is_postnatal", false]], "is_preferred (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.is_preferred", false]], "is_preferred (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.is_preferred", false]], "is_present (gpsea.model.disease property)": [[15, "gpsea.model.Disease.is_present", false]], "is_present (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.is_present", false]], "is_provided() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_provided", false]], "is_structural() (gpsea.model.variantcoordinates method)": [[15, "gpsea.model.VariantCoordinates.is_structural", false]], "is_structural() (gpsea.model.variantinfo method)": [[15, "gpsea.model.VariantInfo.is_structural", false]], "is_structural_deletion() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.is_structural_deletion", false]], "is_structural_variant() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.is_structural_variant", false]], "is_unknown (gpsea.model.vitalstatus property)": [[15, "gpsea.model.VitalStatus.is_unknown", false]], "is_unknown() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_unknown", false]], "iso8601pt (gpsea.model.age attribute)": [[15, "gpsea.model.Age.ISO8601PT", false]], "label (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.label", false]], "label (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.label", false]], "label (gpsea.model.samplelabels property)": [[15, "gpsea.model.SampleLabels.label", false]], "label_summary() (gpsea.model.samplelabels method)": [[15, "gpsea.model.SampleLabels.label_summary", false]], "labels (gpsea.model.patient property)": [[15, "gpsea.model.Patient.labels", false]], "last_menstrual_period() (gpsea.model.age static method)": [[15, "gpsea.model.Age.last_menstrual_period", false]], "list_all_diseases() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_all_diseases", false]], "list_all_proteins() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_all_proteins", false]], "list_all_variants() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_all_variants", false]], "list_measurements() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_measurements", false]], "list_present_phenotypes() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_present_phenotypes", false]], "load_phenopacket_files() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.load_phenopacket_files", false]], "load_phenopacket_folder() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.load_phenopacket_folder", false]], "load_phenopackets() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.load_phenopackets", false]], "logranktest (class in gpsea.analysis.temporal.stats)": [[12, "gpsea.analysis.temporal.stats.LogRankTest", false]], "major_assembly (gpsea.model.genome.genomebuildidentifier property)": [[16, "gpsea.model.genome.GenomeBuildIdentifier.major_assembly", false]], "male (gpsea.model.sex attribute)": [[15, "gpsea.model.Sex.MALE", false]], "mannwhitneystatistic (class in gpsea.analysis.pscore.stats)": [[9, "gpsea.analysis.pscore.stats.MannWhitneyStatistic", false]], "marker_counts (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.marker_counts", false]], "mature_mirna_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.MATURE_MIRNA_VARIANT", false]], "measurement (class in gpsea.model)": [[15, "gpsea.model.Measurement", false]], "measurement_by_id() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.measurement_by_id", false]], "measurementphenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer", false]], "measurements (gpsea.model.patient property)": [[15, "gpsea.model.Patient.measurements", false]], "meta_label (gpsea.model.samplelabels property)": [[15, "gpsea.model.SampleLabels.meta_label", false]], "missense_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.MISSENSE_VARIANT", false]], "mnv (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.MNV", false]], "module": [[0, "module-gpsea", false], [1, "module-gpsea.analysis", false], [2, "module-gpsea.analysis.mtc_filter", false], [3, "module-gpsea.analysis.pcats", false], [4, "module-gpsea.analysis.pcats.stats", false], [5, "module-gpsea.analysis.predicate", false], [6, "module-gpsea.analysis.predicate.genotype", false], [7, "module-gpsea.analysis.predicate.phenotype", false], [8, "module-gpsea.analysis.pscore", false], [9, "module-gpsea.analysis.pscore.stats", false], [10, "module-gpsea.analysis.temporal", false], [11, "module-gpsea.analysis.temporal.endpoint", false], [12, "module-gpsea.analysis.temporal.stats", false], [13, "module-gpsea.config", false], [14, "module-gpsea.io", false], [15, "module-gpsea.model", false], [16, "module-gpsea.model.genome", false], [17, "module-gpsea.preprocessing", false], [18, "module-gpsea.util", false], [19, "module-gpsea.view", false]], "monoallelic_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.monoallelic_predicate", false]], "monophenotypeanalysisresult (class in gpsea.analysis)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult", false]], "motif (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.MOTIF", false]], "motifs() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.motifs", false]], "mtc_correction (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.mtc_correction", false]], "mtc_correction (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.mtc_correction", false]], "mtc_filter_name (gpsea.analysis.pcats.hpotermanalysisresult property)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_filter_name", false]], "mtc_filter_results (gpsea.analysis.pcats.hpotermanalysisresult property)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_filter_results", false]], "mtc_issue (gpsea.analysis.mtc_filter.phenotypemtcresult property)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue", false]], "mtcstatsviewer (class in gpsea.view)": [[19, "gpsea.view.MtcStatsViewer", false]], "multiphenotypeanalysis (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysis", false]], "multiphenotypeanalysisresult (class in gpsea.analysis)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult", false]], "multiphenotypeanalysisresult (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult", false]], "n_categorizations() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.n_categorizations", false]], "n_filtered_out() (gpsea.analysis.pcats.hpotermanalysisresult method)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult.n_filtered_out", false]], "n_significant_for_alpha() (gpsea.analysis.multiphenotypeanalysisresult method)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.n_significant_for_alpha", false]], "n_significant_for_alpha() (gpsea.analysis.pcats.multiphenotypeanalysisresult method)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.n_significant_for_alpha", false]], "n_usable (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.n_usable", false]], "n_usable (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.n_usable", false]], "name (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.name", false]], "name (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.name", false]], "name (gpsea.analysis.pscore.countingphenotypescorer property)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.name", false]], "name (gpsea.analysis.pscore.devriesphenotypescorer property)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.name", false]], "name (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.name", false]], "name (gpsea.model.disease property)": [[15, "gpsea.model.Disease.name", false]], "name (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.name", false]], "name (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.name", false]], "name (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.name", false]], "negative (gpsea.model.genome.strand attribute)": [[16, "gpsea.model.genome.Strand.NEGATIVE", false]], "nmd_transcript_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.NMD_TRANSCRIPT_VARIANT", false]], "no_call (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.NO_CALL", false]], "no_genotype_has_more_than_one_hpo (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO", false]], "non_coding_transcript_exon_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.NON_CODING_TRANSCRIPT_EXON_VARIANT", false]], "non_coding_transcript_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.NON_CODING_TRANSCRIPT_VARIANT", false]], "non_specified_term (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.NON_SPECIFIED_TERM", false]], "noncoding_effects (gpsea.preprocessing.vepfunctionalannotator attribute)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.NONCODING_EFFECTS", false]], "object_hook() (gpsea.io.gpseajsondecoder static method)": [[14, "gpsea.io.GpseaJSONDecoder.object_hook", false]], "observed (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.observed", false]], "ok (gpsea.analysis.mtc_filter.phenotypemtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK", false]], "ok() (gpsea.analysis.mtc_filter.phenotypemtcresult static method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.ok", false]], "one_genotype_has_zero_hpo_observations() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.one_genotype_has_zero_hpo_observations", false]], "onset (gpsea.model.disease property)": [[15, "gpsea.model.Disease.onset", false]], "onset (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.onset", false]], "open_resource() (in module gpsea.util)": [[18, "gpsea.util.open_resource", false]], "open_text_io_handle_for_reading() (in module gpsea.util)": [[18, "gpsea.util.open_text_io_handle_for_reading", false]], "open_text_io_handle_for_writing() (in module gpsea.util)": [[18, "gpsea.util.open_text_io_handle_for_writing", false]], "opposite() (gpsea.model.genome.strand method)": [[16, "gpsea.model.genome.Strand.opposite", false]], "overlapping_exons (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.overlapping_exons", false]], "overlaps_with() (gpsea.model.featureinfo method)": [[15, "gpsea.model.FeatureInfo.overlaps_with", false]], "overlaps_with() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.overlaps_with", false]], "overlaps_with() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.overlaps_with", false]], "parse_multiple() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.parse_multiple", false]], "parse_response() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.parse_response", false]], "parse_uniprot_json() (gpsea.preprocessing.uniprotproteinmetadataservice static method)": [[17, "gpsea.preprocessing.UniprotProteinMetadataService.parse_uniprot_json", false]], "patch (gpsea.model.genome.genomebuildidentifier property)": [[16, "gpsea.model.genome.GenomeBuildIdentifier.patch", false]], "patient (class in gpsea.model)": [[15, "gpsea.model.Patient", false]], "patient_id (gpsea.model.patient property)": [[15, "gpsea.model.Patient.patient_id", false]], "patientcreator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PatientCreator", false]], "ph_col (gpsea.analysis.monophenotypeanalysisresult attribute)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.PH_COL", false]], "pheno_predicates (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.pheno_predicates", false]], "pheno_predicates (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.pheno_predicates", false]], "phenopacketontologytermonsetparser (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser", false]], "phenopacketpatientcreator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PhenopacketPatientCreator", false]], "phenopacketvariantcoordinatefinder (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PhenopacketVariantCoordinateFinder", false]], "phenotype (class in gpsea.model)": [[15, "gpsea.model.Phenotype", false]], "phenotype (gpsea.analysis.monophenotypeanalysisresult property)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.phenotypecategorization property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypeCategorization.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.phenotypepolypredicate property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.phenotype", false]], "phenotype_by_id() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.phenotype_by_id", false]], "phenotype_scorer() (gpsea.analysis.pscore.phenotypescoreanalysisresult method)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult.phenotype_scorer", false]], "phenotypecategorization (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypeCategorization", false]], "phenotypemtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter", false]], "phenotypemtcissue (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcIssue", false]], "phenotypemtcresult (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult", false]], "phenotypepolypredicate (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate", false]], "phenotypes (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.phenotypes", false]], "phenotypes (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.phenotypes", false]], "phenotypes (gpsea.model.patient property)": [[15, "gpsea.model.Patient.phenotypes", false]], "phenotypescoreanalysis (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysis", false]], "phenotypescoreanalysisresult (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult", false]], "phenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.PhenotypeScorer", false]], "phenotypescorestatistic (class in gpsea.analysis.pscore.stats)": [[9, "gpsea.analysis.pscore.stats.PhenotypeScoreStatistic", false]], "plot_boxplots() (gpsea.analysis.pscore.phenotypescoreanalysisresult method)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult.plot_boxplots", false]], "plot_kaplan_meier_curves() (gpsea.analysis.temporal.survivalanalysisresult method)": [[10, "gpsea.analysis.temporal.SurvivalAnalysisResult.plot_kaplan_meier_curves", false]], "policy (gpsea.preprocessing.preprocessingvalidationresult property)": [[17, "gpsea.preprocessing.PreprocessingValidationResult.policy", false]], "polypredicate (class in gpsea.analysis.predicate)": [[5, "gpsea.analysis.predicate.PolyPredicate", false]], "positive (gpsea.model.genome.strand attribute)": [[16, "gpsea.model.genome.Strand.POSITIVE", false]], "possible_results() (gpsea.analysis.mtc_filter.hpomtcfilter method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.possible_results", false]], "possible_results() (gpsea.analysis.mtc_filter.phenotypemtcfilter method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.possible_results", false]], "possible_results() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.possible_results", false]], "possible_results() (gpsea.analysis.mtc_filter.usealltermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.possible_results", false]], "postnatal (gpsea.model.timeline attribute)": [[15, "gpsea.model.Timeline.POSTNATAL", false]], "postnatal() (gpsea.model.age static method)": [[15, "gpsea.model.Age.postnatal", false]], "postnatal_days() (gpsea.model.age static method)": [[15, "gpsea.model.Age.postnatal_days", false]], "postnatal_years() (gpsea.model.age static method)": [[15, "gpsea.model.Age.postnatal_years", false]], "prepare_hpo_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.prepare_hpo_terms_of_interest", false]], "prepare_predicates_for_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest", false]], "preprocessingvalidationresult (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PreprocessingValidationResult", false]], "present_diseases() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.present_diseases", false]], "present_phenotype_categorization (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.present_phenotype_categorization", false]], "present_phenotype_categorization (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.present_phenotype_categorization", false]], "present_phenotype_categorization (gpsea.analysis.predicate.phenotype.phenotypepolypredicate property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.present_phenotype_categorization", false]], "present_phenotype_category (gpsea.analysis.predicate.phenotype.phenotypepolypredicate property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.present_phenotype_category", false]], "present_phenotypes() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.present_phenotypes", false]], "process() (gpsea.preprocessing.cohortcreator method)": [[17, "gpsea.preprocessing.CohortCreator.process", false]], "process() (gpsea.preprocessing.patientcreator method)": [[17, "gpsea.preprocessing.PatientCreator.process", false]], "process() (gpsea.preprocessing.phenopacketontologytermonsetparser method)": [[17, "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser.process", false]], "process() (gpsea.preprocessing.phenopacketpatientcreator method)": [[17, "gpsea.preprocessing.PhenopacketPatientCreator.process", false]], "process() (gpsea.view.cohortvariantviewer method)": [[19, "gpsea.view.CohortVariantViewer.process", false]], "process() (gpsea.view.cohortviewer method)": [[19, "gpsea.view.CohortViewer.process", false]], "process() (gpsea.view.diseaseviewer method)": [[19, "gpsea.view.DiseaseViewer.process", false]], "process() (gpsea.view.mtcstatsviewer method)": [[19, "gpsea.view.MtcStatsViewer.process", false]], "process() (gpsea.view.proteinvariantviewer method)": [[19, "gpsea.view.ProteinVariantViewer.process", false]], "process_response() (gpsea.preprocessing.vepfunctionalannotator method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.process_response", false]], "protcachingmetadataservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ProtCachingMetadataService", false]], "protein_altering_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.PROTEIN_ALTERING_VARIANT", false]], "protein_effect_location (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.protein_effect_location", false]], "protein_feature() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.protein_feature", false]], "protein_feature_ends (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_ends", false]], "protein_feature_names (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_names", false]], "protein_feature_starts (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_starts", false]], "protein_feature_type() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.protein_feature_type", false]], "protein_feature_types (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_types", false]], "protein_features (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.protein_features", false]], "protein_id (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.protein_id", false]], "protein_id (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.protein_id", false]], "protein_id (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_id", false]], "protein_length (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.protein_length", false]], "protein_length (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_length", false]], "protein_metadata (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_metadata", false]], "proteinannotationcache (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ProteinAnnotationCache", false]], "proteinfeature (class in gpsea.model)": [[15, "gpsea.model.ProteinFeature", false]], "proteinmetadata (class in gpsea.model)": [[15, "gpsea.model.ProteinMetadata", false]], "proteinmetadataservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ProteinMetadataService", false]], "proteinvariantviewer (class in gpsea.view)": [[19, "gpsea.view.ProteinVariantViewer", false]], "proteinvisualizable (class in gpsea.view)": [[19, "gpsea.view.ProteinVisualizable", false]], "proteinvisualizer (class in gpsea.view)": [[19, "gpsea.view.ProteinVisualizer", false]], "pval (gpsea.analysis.monophenotypeanalysisresult property)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.pval", false]], "pvals (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.pvals", false]], "pvals (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.pvals", false]], "reason (gpsea.analysis.mtc_filter.phenotypemtcissue attribute)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcIssue.reason", false]], "reason (gpsea.analysis.mtc_filter.phenotypemtcresult property)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason", false]], "ref (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.ref", false]], "ref_length() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.ref_length", false]], "refseq_name (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.refseq_name", false]], "region (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Region", false]], "region (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.region", false]], "region (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.REGION", false]], "region (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.region", false]], "region (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.region", false]], "region() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.region", false]], "regions() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.regions", false]], "regulatory_region_ablation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.REGULATORY_REGION_ABLATION", false]], "regulatory_region_amplification (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.REGULATORY_REGION_AMPLIFICATION", false]], "regulatory_region_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.REGULATORY_REGION_VARIANT", false]], "repeat (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.REPEAT", false]], "repeats() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.repeats", false]], "same_count_as_the_only_child (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SAME_COUNT_AS_THE_ONLY_CHILD", false]], "samplelabels (class in gpsea.model)": [[15, "gpsea.model.SampleLabels", false]], "score() (gpsea.analysis.pscore.countingphenotypescorer method)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.score", false]], "score() (gpsea.analysis.pscore.devriesphenotypescorer method)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.score", false]], "score() (gpsea.analysis.pscore.measurementphenotypescorer method)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.score", false]], "score() (gpsea.analysis.pscore.phenotypescorer method)": [[8, "gpsea.analysis.pscore.PhenotypeScorer.score", false]], "sequence_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SEQUENCE_VARIANT", false]], "sex (class in gpsea.model)": [[15, "gpsea.model.Sex", false]], "sex (gpsea.model.patient property)": [[15, "gpsea.model.Patient.sex", false]], "sex_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.sex_predicate", false]], "significant_phenotype_indices() (gpsea.analysis.multiphenotypeanalysisresult method)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.significant_phenotype_indices", false]], "significant_phenotype_indices() (gpsea.analysis.pcats.multiphenotypeanalysisresult method)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.significant_phenotype_indices", false]], "single() (gpsea.model.genotypes static method)": [[15, "gpsea.model.Genotypes.single", false]], "skipping_general_term (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_GENERAL_TERM", false]], "skipping_non_phenotype_term (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_NON_PHENOTYPE_TERM", false]], "skipping_since_one_genotype_had_zero_observations (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS", false]], "snv (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.SNV", false]], "some_cell_has_greater_than_one_count() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.some_cell_has_greater_than_one_count", false]], "specifiedtermsmtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter", false]], "splice_acceptor_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_ACCEPTOR_VARIANT", false]], "splice_donor_5th_base_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_DONOR_5TH_BASE_VARIANT", false]], "splice_donor_region_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_DONOR_REGION_VARIANT", false]], "splice_donor_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_DONOR_VARIANT", false]], "splice_polypyrimidine_tract_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_POLYPYRIMIDINE_TRACT_VARIANT", false]], "splice_region_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_REGION_VARIANT", false]], "start (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.start", false]], "start (gpsea.model.genome.region property)": [[16, "gpsea.model.genome.Region.start", false]], "start (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.start", false]], "start_lost (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.START_LOST", false]], "start_on_strand() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.start_on_strand", false]], "start_retained_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.START_RETAINED_VARIANT", false]], "statistic (gpsea.analysis.analysisresult property)": [[1, "gpsea.analysis.AnalysisResult.statistic", false]], "status (class in gpsea.model)": [[15, "gpsea.model.Status", false]], "status (gpsea.model.vitalstatus attribute)": [[15, "gpsea.model.VitalStatus.status", false]], "stop_gained (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.STOP_GAINED", false]], "stop_lost (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.STOP_LOST", false]], "stop_retained_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.STOP_RETAINED_VARIANT", false]], "store_annotations() (gpsea.preprocessing.proteinannotationcache method)": [[17, "gpsea.preprocessing.ProteinAnnotationCache.store_annotations", false]], "store_annotations() (gpsea.preprocessing.variantannotationcache method)": [[17, "gpsea.preprocessing.VariantAnnotationCache.store_annotations", false]], "strand (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Strand", false]], "strand (gpsea.model.genome.genomicregion property)": [[16, "gpsea.model.genome.GenomicRegion.strand", false]], "strand (gpsea.model.genome.stranded property)": [[16, "gpsea.model.genome.Stranded.strand", false]], "stranded (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Stranded", false]], "structural_so_id_to_display() (gpsea.model.varianteffect static method)": [[15, "gpsea.model.VariantEffect.structural_so_id_to_display", false]], "structural_type (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.structural_type", false]], "structural_type() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.structural_type", false]], "summarize() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.summarize", false]], "summarize() (gpsea.preprocessing.preprocessingvalidationresult method)": [[17, "gpsea.preprocessing.PreprocessingValidationResult.summarize", false]], "summarize_groups() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.summarize_groups", false]], "summarize_hpo_analysis() (in module gpsea.view)": [[19, "gpsea.view.summarize_hpo_analysis", false]], "supports_shape (gpsea.analysis.pcats.stats.countstatistic property)": [[4, "gpsea.analysis.pcats.stats.CountStatistic.supports_shape", false]], "supports_shape (gpsea.analysis.pcats.stats.fisherexacttest property)": [[4, "gpsea.analysis.pcats.stats.FisherExactTest.supports_shape", false]], "survival (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.Survival", false]], "survivalanalysis (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.SurvivalAnalysis", false]], "survivalanalysisresult (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.SurvivalAnalysisResult", false]], "survivalstatistic (class in gpsea.analysis.temporal.stats)": [[12, "gpsea.analysis.temporal.stats.SurvivalStatistic", false]], "sv_info (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.sv_info", false]], "symbol (gpsea.model.genome.strand property)": [[16, "gpsea.model.genome.Strand.symbol", false]], "synonymous_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SYNONYMOUS_VARIANT", false]], "term_id (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.term_id", false]], "terms_to_test (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter property)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.terms_to_test", false]], "test() (gpsea.analysis.predicate.genotype.variantpredicate method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicate.test", false]], "test() (gpsea.analysis.predicate.phenotype.diseasepresencepredicate method)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.test", false]], "test() (gpsea.analysis.predicate.phenotype.hpopredicate method)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.test", false]], "test() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.test", false]], "test_result (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.test_result", false]], "tf_binding_site_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TF_BINDING_SITE_VARIANT", false]], "tfbs_ablation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TFBS_ABLATION", false]], "tfbs_amplification (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TFBS_AMPLIFICATION", false]], "three_prime_utr_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.THREE_PRIME_UTR_VARIANT", false]], "timeline (class in gpsea.model)": [[15, "gpsea.model.Timeline", false]], "timeline (gpsea.model.age property)": [[15, "gpsea.model.Age.timeline", false]], "to_display() (gpsea.model.varianteffect method)": [[15, "gpsea.model.VariantEffect.to_display", false]], "to_negative_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.to_negative_strand", false]], "to_opposite_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.to_opposite_strand", false]], "to_positive_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.to_positive_strand", false]], "to_string() (gpsea.model.proteinfeature method)": [[15, "gpsea.model.ProteinFeature.to_string", false]], "total_patient_count (gpsea.model.cohort property)": [[15, "gpsea.model.Cohort.total_patient_count", false]], "total_tests (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.total_tests", false]], "total_tests (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.total_tests", false]], "transcript() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.transcript", false]], "transcript_ablation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TRANSCRIPT_ABLATION", false]], "transcript_amplification (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TRANSCRIPT_AMPLIFICATION", false]], "transcript_coordinates (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.transcript_coordinates", false]], "transcript_id (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.transcript_id", false]], "transcript_id (gpsea.model.transcriptinfoaware property)": [[15, "gpsea.model.TranscriptInfoAware.transcript_id", false]], "transcript_id (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.transcript_id", false]], "transcriptannotation (class in gpsea.model)": [[15, "gpsea.model.TranscriptAnnotation", false]], "transcriptcoordinates (class in gpsea.model)": [[15, "gpsea.model.TranscriptCoordinates", false]], "transcriptcoordinateservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.TranscriptCoordinateService", false]], "transcriptinfoaware (class in gpsea.model)": [[15, "gpsea.model.TranscriptInfoAware", false]], "translocation (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.TRANSLOCATION", false]], "transposable (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Transposable", false]], "transpose_coordinate() (in module gpsea.model.genome)": [[16, "gpsea.model.genome.transpose_coordinate", false]], "true() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.true", false]], "tteststatistic (class in gpsea.analysis.pscore.stats)": [[9, "gpsea.analysis.pscore.stats.TTestStatistic", false]], "tx_annotations (gpsea.model.functionalannotationaware property)": [[15, "gpsea.model.FunctionalAnnotationAware.tx_annotations", false]], "tx_annotations (gpsea.model.variant property)": [[15, "gpsea.model.Variant.tx_annotations", false]], "ucsc_name (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.ucsc_name", false]], "uniprotproteinmetadataservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.UniprotProteinMetadataService", false]], "unit (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.unit", false]], "unknown (gpsea.model.status attribute)": [[15, "gpsea.model.Status.UNKNOWN", false]], "unknown_sex (gpsea.model.sex attribute)": [[15, "gpsea.model.Sex.UNKNOWN_SEX", false]], "upstream_gene_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.UPSTREAM_GENE_VARIANT", false]], "usealltermsmtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter", false]], "value (gpsea.analysis.temporal.survival attribute)": [[10, "gpsea.analysis.temporal.Survival.value", false]], "varcachingfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VarCachingFunctionalAnnotator", false]], "variable_name (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.variable_name", false]], "variable_name (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.variable_name", false]], "variable_name (gpsea.analysis.pscore.countingphenotypescorer property)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.variable_name", false]], "variable_name (gpsea.analysis.pscore.devriesphenotypescorer property)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.variable_name", false]], "variable_name (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.variable_name", false]], "variant (class in gpsea.model)": [[15, "gpsea.model.Variant", false]], "variant_class (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.variant_class", false]], "variant_class (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.variant_class", false]], "variant_class (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.variant_class", false]], "variant_class() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.variant_class", false]], "variant_coordinates (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.variant_coordinates", false]], "variant_effect() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.variant_effect", false]], "variant_effect_count_by_tx() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.variant_effect_count_by_tx", false]], "variant_effects (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.variant_effects", false]], "variant_effects (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.variant_effects", false]], "variant_info (gpsea.model.variant property)": [[15, "gpsea.model.Variant.variant_info", false]], "variant_info (gpsea.model.variantinfoaware property)": [[15, "gpsea.model.VariantInfoAware.variant_info", false]], "variant_key (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.variant_key", false]], "variant_key (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.variant_key", false]], "variant_key (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.variant_key", false]], "variant_key() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.variant_key", false]], "variant_locations (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.variant_locations", false]], "variant_locations_counted_absolute (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.variant_locations_counted_absolute", false]], "variantannotationcache (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VariantAnnotationCache", false]], "variantclass (class in gpsea.model)": [[15, "gpsea.model.VariantClass", false]], "variantcoordinatefinder (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VariantCoordinateFinder", false]], "variantcoordinates (class in gpsea.model)": [[15, "gpsea.model.VariantCoordinates", false]], "varianteffect (class in gpsea.model)": [[15, "gpsea.model.VariantEffect", false]], "variantformatter (class in gpsea.view)": [[19, "gpsea.view.VariantFormatter", false]], "variantinfo (class in gpsea.model)": [[15, "gpsea.model.VariantInfo", false]], "variantinfoaware (class in gpsea.model)": [[15, "gpsea.model.VariantInfoAware", false]], "variantpredicate (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicate", false]], "variantpredicates (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates", false]], "variants (gpsea.model.patient property)": [[15, "gpsea.model.Patient.variants", false]], "varianttranscriptvisualizer (class in gpsea.view)": [[19, "gpsea.view.VariantTranscriptVisualizer", false]], "vepfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator", false]], "verify_term_id() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.verify_term_id", false]], "vital_status (gpsea.model.patient property)": [[15, "gpsea.model.Patient.vital_status", false]], "vitalstatus (class in gpsea.model)": [[15, "gpsea.model.VitalStatus", false]], "vvhgvsvariantcoordinatefinder (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VVHgvsVariantCoordinateFinder", false]], "vvmulticoordinateservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VVMultiCoordinateService", false]], "with_cache_folder() (gpsea.preprocessing.varcachingfunctionalannotator static method)": [[17, "gpsea.preprocessing.VarCachingFunctionalAnnotator.with_cache_folder", false]], "with_strand() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.with_strand", false]], "with_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.with_strand", false]], "wrap_scoring_function() (gpsea.analysis.pscore.phenotypescorer static method)": [[8, "gpsea.analysis.pscore.PhenotypeScorer.wrap_scoring_function", false]], "write() (gpsea.view.gpseareport method)": [[19, "gpsea.view.GpseaReport.write", false]], "zinc_finger (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.ZINC_FINGER", false]]}, "objects": {"": [[0, 0, 0, "-", "gpsea"]], "gpsea": [[1, 0, 0, "-", "analysis"], [13, 0, 0, "-", "config"], [14, 0, 0, "-", "io"], [15, 0, 0, "-", "model"], [17, 0, 0, "-", "preprocessing"], [18, 0, 0, "-", "util"], [19, 0, 0, "-", "view"]], "gpsea.analysis": [[1, 1, 1, "", "AnalysisResult"], [1, 1, 1, "", "MonoPhenotypeAnalysisResult"], [1, 1, 1, "", "MultiPhenotypeAnalysisResult"], [2, 0, 0, "-", "mtc_filter"], [3, 0, 0, "-", "pcats"], [5, 0, 0, "-", "predicate"], [8, 0, 0, "-", "pscore"], [10, 0, 0, "-", "temporal"]], "gpsea.analysis.AnalysisResult": [[1, 2, 1, "", "gt_predicate"], [1, 2, 1, "", "statistic"]], "gpsea.analysis.MonoPhenotypeAnalysisResult": [[1, 3, 1, "", "DATA_COLUMNS"], [1, 3, 1, "", "GT_COL"], [1, 3, 1, "", "PH_COL"], [1, 4, 1, "", "complete_records"], [1, 2, 1, "", "data"], [1, 2, 1, "", "phenotype"], [1, 2, 1, "", "pval"]], "gpsea.analysis.MultiPhenotypeAnalysisResult": [[1, 2, 1, "", "all_counts"], [1, 2, 1, "", "corrected_pvals"], [1, 2, 1, "", "mtc_correction"], [1, 4, 1, "", "n_significant_for_alpha"], [1, 2, 1, "", "n_usable"], [1, 2, 1, "", "pheno_predicates"], [1, 2, 1, "", "phenotypes"], [1, 2, 1, "", "pvals"], [1, 4, 1, "", "significant_phenotype_indices"], [1, 2, 1, "", "total_tests"]], "gpsea.analysis.mtc_filter": [[2, 1, 1, "", "HpoMtcFilter"], [2, 1, 1, "", "PhenotypeMtcFilter"], [2, 1, 1, "", "PhenotypeMtcIssue"], [2, 1, 1, "", "PhenotypeMtcResult"], [2, 1, 1, "", "SpecifiedTermsMtcFilter"], [2, 1, 1, "", "UseAllTermsMtcFilter"]], "gpsea.analysis.mtc_filter.HpoMtcFilter": [[2, 3, 1, "", "NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO"], [2, 3, 1, "", "SAME_COUNT_AS_THE_ONLY_CHILD"], [2, 3, 1, "", "SKIPPING_GENERAL_TERM"], [2, 3, 1, "", "SKIPPING_NON_PHENOTYPE_TERM"], [2, 3, 1, "", "SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS"], [2, 4, 1, "", "default_filter"], [2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "get_maximum_group_observed_HPO_frequency"], [2, 4, 1, "", "get_number_of_observed_hpo_observations"], [2, 4, 1, "", "one_genotype_has_zero_hpo_observations"], [2, 4, 1, "", "possible_results"], [2, 4, 1, "", "some_cell_has_greater_than_one_count"]], "gpsea.analysis.mtc_filter.PhenotypeMtcFilter": [[2, 3, 1, "", "OK"], [2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "possible_results"]], "gpsea.analysis.mtc_filter.PhenotypeMtcIssue": [[2, 3, 1, "", "code"], [2, 3, 1, "", "reason"]], "gpsea.analysis.mtc_filter.PhenotypeMtcResult": [[2, 4, 1, "", "fail"], [2, 4, 1, "", "is_filtered_out"], [2, 4, 1, "", "is_passed"], [2, 2, 1, "", "mtc_issue"], [2, 4, 1, "", "ok"], [2, 2, 1, "", "reason"]], "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter": [[2, 3, 1, "", "NON_SPECIFIED_TERM"], [2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "possible_results"], [2, 2, 1, "", "terms_to_test"], [2, 4, 1, "", "verify_term_id"]], "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter": [[2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "possible_results"]], "gpsea.analysis.pcats": [[3, 1, 1, "", "DiseaseAnalysis"], [3, 1, 1, "", "HpoTermAnalysis"], [3, 1, 1, "", "HpoTermAnalysisResult"], [3, 1, 1, "", "MultiPhenotypeAnalysis"], [3, 1, 1, "", "MultiPhenotypeAnalysisResult"], [3, 5, 1, "", "apply_predicates_on_patients"], [3, 5, 1, "", "configure_hpo_term_analysis"], [4, 0, 0, "-", "stats"]], "gpsea.analysis.pcats.HpoTermAnalysisResult": [[3, 2, 1, "", "mtc_filter_name"], [3, 2, 1, "", "mtc_filter_results"], [3, 4, 1, "", "n_filtered_out"]], "gpsea.analysis.pcats.MultiPhenotypeAnalysis": [[3, 4, 1, "", "compare_genotype_vs_phenotypes"]], "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult": [[3, 2, 1, "", "all_counts"], [3, 2, 1, "", "corrected_pvals"], [3, 2, 1, "", "mtc_correction"], [3, 4, 1, "", "n_significant_for_alpha"], [3, 2, 1, "", "n_usable"], [3, 2, 1, "", "pheno_predicates"], [3, 2, 1, "", "phenotypes"], [3, 2, 1, "", "pvals"], [3, 4, 1, "", "significant_phenotype_indices"], [3, 2, 1, "", "total_tests"]], "gpsea.analysis.pcats.stats": [[4, 1, 1, "", "CountStatistic"], [4, 1, 1, "", "FisherExactTest"]], "gpsea.analysis.pcats.stats.CountStatistic": [[4, 4, 1, "", "compute_pval"], [4, 2, 1, "", "supports_shape"]], "gpsea.analysis.pcats.stats.FisherExactTest": [[4, 4, 1, "", "compute_pval"], [4, 2, 1, "", "supports_shape"]], "gpsea.analysis.predicate": [[5, 1, 1, "", "PolyPredicate"], [6, 0, 0, "-", "genotype"], [7, 0, 0, "-", "phenotype"]], "gpsea.analysis.predicate.PolyPredicate": [[5, 4, 1, "", "get_categories"], [5, 4, 1, "", "get_categorizations"], [5, 4, 1, "", "get_category"], [5, 4, 1, "", "get_category_name"], [5, 2, 1, "", "group_labels"], [5, 4, 1, "", "n_categorizations"], [5, 4, 1, "", "summarize"], [5, 4, 1, "", "summarize_groups"], [5, 4, 1, "", "test"]], "gpsea.analysis.predicate.genotype": [[6, 1, 1, "", "AlleleCounter"], [6, 1, 1, "", "GenotypePolyPredicate"], [6, 1, 1, "", "VariantPredicate"], [6, 1, 1, "", "VariantPredicates"], [6, 5, 1, "", "allele_count"], [6, 5, 1, "", "biallelic_predicate"], [6, 5, 1, "", "diagnosis_predicate"], [6, 5, 1, "", "monoallelic_predicate"], [6, 5, 1, "", "sex_predicate"]], "gpsea.analysis.predicate.genotype.AlleleCounter": [[6, 4, 1, "", "count"], [6, 4, 1, "", "get_question"]], "gpsea.analysis.predicate.genotype.VariantPredicate": [[6, 4, 1, "", "get_question"], [6, 4, 1, "", "test"]], "gpsea.analysis.predicate.genotype.VariantPredicates": [[6, 4, 1, "", "all"], [6, 4, 1, "", "any"], [6, 4, 1, "", "change_length"], [6, 4, 1, "", "exon"], [6, 4, 1, "", "gene"], [6, 4, 1, "", "is_large_imprecise_sv"], [6, 4, 1, "", "is_structural_deletion"], [6, 4, 1, "", "is_structural_variant"], [6, 4, 1, "", "protein_feature"], [6, 4, 1, "", "protein_feature_type"], [6, 4, 1, "", "ref_length"], [6, 4, 1, "", "region"], [6, 4, 1, "", "structural_type"], [6, 4, 1, "", "transcript"], [6, 4, 1, "", "true"], [6, 4, 1, "", "variant_class"], [6, 4, 1, "", "variant_effect"], [6, 4, 1, "", "variant_key"]], "gpsea.analysis.predicate.phenotype": [[7, 1, 1, "", "DiseasePresencePredicate"], [7, 1, 1, "", "HpoPredicate"], [7, 1, 1, "", "PhenotypeCategorization"], [7, 1, 1, "", "PhenotypePolyPredicate"], [7, 5, 1, "", "prepare_hpo_terms_of_interest"], [7, 5, 1, "", "prepare_predicates_for_terms_of_interest"]], "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate": [[7, 2, 1, "", "description"], [7, 4, 1, "", "get_categorizations"], [7, 2, 1, "", "name"], [7, 2, 1, "", "phenotype"], [7, 2, 1, "", "present_phenotype_categorization"], [7, 4, 1, "", "test"], [7, 2, 1, "", "variable_name"]], "gpsea.analysis.predicate.phenotype.HpoPredicate": [[7, 2, 1, "", "description"], [7, 4, 1, "", "get_categorizations"], [7, 2, 1, "", "name"], [7, 2, 1, "", "phenotype"], [7, 2, 1, "", "present_phenotype_categorization"], [7, 4, 1, "", "test"], [7, 2, 1, "", "variable_name"]], "gpsea.analysis.predicate.phenotype.PhenotypeCategorization": [[7, 2, 1, "", "phenotype"]], "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate": [[7, 2, 1, "", "phenotype"], [7, 2, 1, "", "present_phenotype_categorization"], [7, 2, 1, "", "present_phenotype_category"]], "gpsea.analysis.pscore": [[8, 1, 1, "", "CountingPhenotypeScorer"], [8, 1, 1, "", "DeVriesPhenotypeScorer"], [8, 1, 1, "", "MeasurementPhenotypeScorer"], [8, 1, 1, "", "PhenotypeScoreAnalysis"], [8, 1, 1, "", "PhenotypeScoreAnalysisResult"], [8, 1, 1, "", "PhenotypeScorer"], [9, 0, 0, "-", "stats"]], "gpsea.analysis.pscore.CountingPhenotypeScorer": [[8, 2, 1, "", "description"], [8, 4, 1, "", "from_query_curies"], [8, 2, 1, "", "name"], [8, 4, 1, "", "score"], [8, 2, 1, "", "variable_name"]], "gpsea.analysis.pscore.DeVriesPhenotypeScorer": [[8, 2, 1, "", "description"], [8, 2, 1, "", "name"], [8, 4, 1, "", "score"], [8, 2, 1, "", "variable_name"]], "gpsea.analysis.pscore.MeasurementPhenotypeScorer": [[8, 2, 1, "", "description"], [8, 4, 1, "", "from_measurement_id"], [8, 2, 1, "", "label"], [8, 2, 1, "", "name"], [8, 4, 1, "", "score"], [8, 2, 1, "", "term_id"], [8, 2, 1, "", "variable_name"]], "gpsea.analysis.pscore.PhenotypeScoreAnalysis": [[8, 4, 1, "", "compare_genotype_vs_phenotype_score"]], "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult": [[8, 4, 1, "", "phenotype_scorer"], [8, 4, 1, "", "plot_boxplots"]], "gpsea.analysis.pscore.PhenotypeScorer": [[8, 4, 1, "", "score"], [8, 4, 1, "", "wrap_scoring_function"]], "gpsea.analysis.pscore.stats": [[9, 1, 1, "", "MannWhitneyStatistic"], [9, 1, 1, "", "PhenotypeScoreStatistic"], [9, 1, 1, "", "TTestStatistic"]], "gpsea.analysis.pscore.stats.MannWhitneyStatistic": [[9, 4, 1, "", "compute_pval"]], "gpsea.analysis.pscore.stats.PhenotypeScoreStatistic": [[9, 4, 1, "", "compute_pval"]], "gpsea.analysis.pscore.stats.TTestStatistic": [[9, 4, 1, "", "compute_pval"]], "gpsea.analysis.temporal": [[10, 1, 1, "", "Endpoint"], [10, 1, 1, "", "Survival"], [10, 1, 1, "", "SurvivalAnalysis"], [10, 1, 1, "", "SurvivalAnalysisResult"], [11, 0, 0, "-", "endpoint"], [12, 0, 0, "-", "stats"]], "gpsea.analysis.temporal.Endpoint": [[10, 4, 1, "", "compute_survival"]], "gpsea.analysis.temporal.Survival": [[10, 3, 1, "", "is_censored"], [10, 3, 1, "", "value"]], "gpsea.analysis.temporal.SurvivalAnalysis": [[10, 4, 1, "", "compare_genotype_vs_survival"]], "gpsea.analysis.temporal.SurvivalAnalysisResult": [[10, 2, 1, "", "endpoint"], [10, 4, 1, "", "plot_kaplan_meier_curves"]], "gpsea.analysis.temporal.endpoint": [[11, 5, 1, "", "death"], [11, 5, 1, "", "disease_onset"], [11, 5, 1, "", "hpo_onset"]], "gpsea.analysis.temporal.stats": [[12, 1, 1, "", "LogRankTest"], [12, 1, 1, "", "SurvivalStatistic"]], "gpsea.analysis.temporal.stats.LogRankTest": [[12, 4, 1, "", "compute_pval"]], "gpsea.analysis.temporal.stats.SurvivalStatistic": [[12, 4, 1, "", "compute_pval"]], "gpsea.config": [[13, 6, 1, "", "CACHE_ENV"], [13, 6, 1, "", "DEFAULT_CACHE_PATH"], [13, 5, 1, "", "get_cache_dir_path"]], "gpsea.io": [[14, 1, 1, "", "GpseaJSONDecoder"], [14, 1, 1, "", "GpseaJSONEncoder"]], "gpsea.io.GpseaJSONDecoder": [[14, 4, 1, "", "object_hook"]], "gpsea.io.GpseaJSONEncoder": [[14, 4, 1, "", "default"]], "gpsea.model": [[15, 1, 1, "", "Age"], [15, 1, 1, "", "Cohort"], [15, 1, 1, "", "Disease"], [15, 1, 1, "", "FeatureInfo"], [15, 1, 1, "", "FeatureType"], [15, 1, 1, "", "FunctionalAnnotationAware"], [15, 1, 1, "", "Genotype"], [15, 1, 1, "", "Genotyped"], [15, 1, 1, "", "Genotypes"], [15, 1, 1, "", "ImpreciseSvInfo"], [15, 1, 1, "", "Measurement"], [15, 1, 1, "", "Patient"], [15, 1, 1, "", "Phenotype"], [15, 1, 1, "", "ProteinFeature"], [15, 1, 1, "", "ProteinMetadata"], [15, 1, 1, "", "SampleLabels"], [15, 1, 1, "", "Sex"], [15, 1, 1, "", "Status"], [15, 1, 1, "", "Timeline"], [15, 1, 1, "", "TranscriptAnnotation"], [15, 1, 1, "", "TranscriptCoordinates"], [15, 1, 1, "", "TranscriptInfoAware"], [15, 1, 1, "", "Variant"], [15, 1, 1, "", "VariantClass"], [15, 1, 1, "", "VariantCoordinates"], [15, 1, 1, "", "VariantEffect"], [15, 1, 1, "", "VariantInfo"], [15, 1, 1, "", "VariantInfoAware"], [15, 1, 1, "", "VitalStatus"], [16, 0, 0, "-", "genome"]], "gpsea.model.Age": [[15, 3, 1, "", "DAYS_IN_MONTH"], [15, 3, 1, "", "DAYS_IN_WEEK"], [15, 3, 1, "", "DAYS_IN_YEAR"], [15, 3, 1, "", "ISO8601PT"], [15, 4, 1, "", "birth"], [15, 2, 1, "", "days"], [15, 4, 1, "", "from_iso8601_period"], [15, 4, 1, "", "gestational"], [15, 4, 1, "", "gestational_days"], [15, 2, 1, "", "is_gestational"], [15, 2, 1, "", "is_postnatal"], [15, 4, 1, "", "last_menstrual_period"], [15, 4, 1, "", "postnatal"], [15, 4, 1, "", "postnatal_days"], [15, 4, 1, "", "postnatal_years"], [15, 2, 1, "", "timeline"]], "gpsea.model.Cohort": [[15, 4, 1, "", "all_diseases"], [15, 4, 1, "", "all_measurements"], [15, 2, 1, "", "all_patients"], [15, 4, 1, "", "all_phenotypes"], [15, 2, 1, "", "all_transcript_ids"], [15, 4, 1, "", "all_variant_infos"], [15, 4, 1, "", "all_variants"], [15, 4, 1, "", "count_alive"], [15, 4, 1, "", "count_deceased"], [15, 4, 1, "", "count_distinct_diseases"], [15, 4, 1, "", "count_distinct_hpo_terms"], [15, 4, 1, "", "count_distinct_measurements"], [15, 4, 1, "", "count_females"], [15, 4, 1, "", "count_males"], [15, 4, 1, "", "count_unknown_sex"], [15, 4, 1, "", "count_unknown_vital_status"], [15, 4, 1, "", "count_with_age_of_last_encounter"], [15, 4, 1, "", "count_with_disease_onset"], [15, 4, 1, "", "from_patients"], [15, 4, 1, "", "get_excluded_count"], [15, 4, 1, "", "get_patient_ids"], [15, 4, 1, "", "get_variant_by_key"], [15, 4, 1, "", "list_all_diseases"], [15, 4, 1, "", "list_all_proteins"], [15, 4, 1, "", "list_all_variants"], [15, 4, 1, "", "list_measurements"], [15, 4, 1, "", "list_present_phenotypes"], [15, 2, 1, "", "total_patient_count"], [15, 4, 1, "", "variant_effect_count_by_tx"]], "gpsea.model.Disease": [[15, 4, 1, "", "from_raw_parts"], [15, 2, 1, "", "identifier"], [15, 2, 1, "", "is_present"], [15, 2, 1, "", "name"], [15, 2, 1, "", "onset"]], "gpsea.model.FeatureInfo": [[15, 2, 1, "", "end"], [15, 2, 1, "", "name"], [15, 4, 1, "", "overlaps_with"], [15, 2, 1, "", "region"], [15, 2, 1, "", "start"]], "gpsea.model.FeatureType": [[15, 3, 1, "", "COILED_COIL"], [15, 3, 1, "", "COMPOSITIONAL_BIAS"], [15, 3, 1, "", "DOMAIN"], [15, 3, 1, "", "MOTIF"], [15, 3, 1, "", "REGION"], [15, 3, 1, "", "REPEAT"], [15, 3, 1, "", "ZINC_FINGER"], [15, 4, 1, "", "from_string"]], "gpsea.model.FunctionalAnnotationAware": [[15, 4, 1, "", "get_hgvs_cdna_by_tx_id"], [15, 4, 1, "", "get_preferred_tx_annotation"], [15, 4, 1, "", "get_tx_anno_by_tx_id"], [15, 2, 1, "", "tx_annotations"]], "gpsea.model.Genotype": [[15, 3, 1, "", "HEMIZYGOUS"], [15, 3, 1, "", "HETEROZYGOUS"], [15, 3, 1, "", "HOMOZYGOUS_ALTERNATE"], [15, 3, 1, "", "HOMOZYGOUS_REFERENCE"], [15, 3, 1, "", "NO_CALL"], [15, 2, 1, "", "code"]], "gpsea.model.Genotyped": [[15, 4, 1, "", "genotype_for_sample"], [15, 2, 1, "", "genotypes"]], "gpsea.model.Genotypes": [[15, 4, 1, "", "empty"], [15, 4, 1, "", "for_sample"], [15, 4, 1, "", "from_mapping"], [15, 4, 1, "", "single"]], "gpsea.model.ImpreciseSvInfo": [[15, 2, 1, "", "gene_id"], [15, 2, 1, "", "gene_symbol"], [15, 2, 1, "", "structural_type"], [15, 2, 1, "", "variant_class"], [15, 2, 1, "", "variant_key"]], "gpsea.model.Measurement": [[15, 2, 1, "", "identifier"], [15, 2, 1, "", "name"], [15, 2, 1, "", "test_result"], [15, 2, 1, "", "unit"]], "gpsea.model.Patient": [[15, 2, 1, "", "age"], [15, 4, 1, "", "count_unique_diseases"], [15, 4, 1, "", "count_unique_measurements"], [15, 4, 1, "", "count_unique_phenotypes"], [15, 4, 1, "", "disease_by_id"], [15, 2, 1, "", "diseases"], [15, 4, 1, "", "excluded_diseases"], [15, 4, 1, "", "excluded_phenotypes"], [15, 4, 1, "", "from_raw_parts"], [15, 2, 1, "", "labels"], [15, 4, 1, "", "measurement_by_id"], [15, 2, 1, "", "measurements"], [15, 2, 1, "", "patient_id"], [15, 4, 1, "", "phenotype_by_id"], [15, 2, 1, "", "phenotypes"], [15, 4, 1, "", "present_diseases"], [15, 4, 1, "", "present_phenotypes"], [15, 2, 1, "", "sex"], [15, 2, 1, "", "variants"], [15, 2, 1, "", "vital_status"]], "gpsea.model.Phenotype": [[15, 4, 1, "", "from_raw_parts"], [15, 4, 1, "", "from_term"], [15, 2, 1, "", "identifier"], [15, 2, 1, "", "is_observed"], [15, 2, 1, "", "is_present"], [15, 2, 1, "", "observed"], [15, 2, 1, "", "onset"]], "gpsea.model.ProteinFeature": [[15, 4, 1, "", "create"], [15, 2, 1, "", "feature_type"], [15, 2, 1, "", "info"], [15, 4, 1, "", "to_string"]], "gpsea.model.ProteinMetadata": [[15, 4, 1, "", "domains"], [15, 4, 1, "", "from_feature_frame"], [15, 4, 1, "", "from_uniprot_json"], [15, 4, 1, "", "get_features_variant_overlaps"], [15, 2, 1, "", "label"], [15, 4, 1, "", "motifs"], [15, 2, 1, "", "protein_features"], [15, 2, 1, "", "protein_id"], [15, 2, 1, "", "protein_length"], [15, 4, 1, "", "regions"], [15, 4, 1, "", "repeats"]], "gpsea.model.SampleLabels": [[15, 2, 1, "", "label"], [15, 4, 1, "", "label_summary"], [15, 2, 1, "", "meta_label"]], "gpsea.model.Sex": [[15, 3, 1, "", "FEMALE"], [15, 3, 1, "", "MALE"], [15, 3, 1, "", "UNKNOWN_SEX"], [15, 4, 1, "", "is_female"], [15, 4, 1, "", "is_male"], [15, 4, 1, "", "is_provided"], [15, 4, 1, "", "is_unknown"]], "gpsea.model.Status": [[15, 3, 1, "", "ALIVE"], [15, 3, 1, "", "DECEASED"], [15, 3, 1, "", "UNKNOWN"]], "gpsea.model.Timeline": [[15, 3, 1, "", "GESTATIONAL"], [15, 3, 1, "", "POSTNATAL"]], "gpsea.model.TranscriptAnnotation": [[15, 2, 1, "", "gene_id"], [15, 2, 1, "", "hgvs_cdna"], [15, 2, 1, "", "hgvsp"], [15, 2, 1, "", "is_preferred"], [15, 2, 1, "", "overlapping_exons"], [15, 2, 1, "", "protein_effect_location"], [15, 2, 1, "", "protein_id"], [15, 2, 1, "", "transcript_id"], [15, 2, 1, "", "variant_effects"]], "gpsea.model.TranscriptCoordinates": [[15, 2, 1, "", "cds_end"], [15, 2, 1, "", "cds_start"], [15, 2, 1, "", "exons"], [15, 4, 1, "", "get_cds_regions"], [15, 4, 1, "", "get_coding_base_count"], [15, 4, 1, "", "get_codon_count"], [15, 4, 1, "", "get_five_prime_utrs"], [15, 4, 1, "", "get_three_prime_utrs"], [15, 2, 1, "", "identifier"], [15, 4, 1, "", "is_coding"], [15, 2, 1, "", "is_preferred"], [15, 2, 1, "", "region"]], "gpsea.model.TranscriptInfoAware": [[15, 2, 1, "", "gene_id"], [15, 2, 1, "", "transcript_id"]], "gpsea.model.Variant": [[15, 4, 1, "", "create_variant_from_scratch"], [15, 2, 1, "", "genotypes"], [15, 2, 1, "", "tx_annotations"], [15, 2, 1, "", "variant_info"]], "gpsea.model.VariantClass": [[15, 3, 1, "", "DEL"], [15, 3, 1, "", "DUP"], [15, 3, 1, "", "INS"], [15, 3, 1, "", "INV"], [15, 3, 1, "", "MNV"], [15, 3, 1, "", "SNV"], [15, 3, 1, "", "TRANSLOCATION"]], "gpsea.model.VariantCoordinates": [[15, 2, 1, "", "alt"], [15, 2, 1, "", "change_length"], [15, 2, 1, "", "chrom"], [15, 2, 1, "", "end"], [15, 4, 1, "", "from_vcf_literal"], [15, 4, 1, "", "from_vcf_symbolic"], [15, 4, 1, "", "is_structural"], [15, 2, 1, "", "ref"], [15, 2, 1, "", "region"], [15, 2, 1, "", "start"], [15, 2, 1, "", "variant_class"], [15, 2, 1, "", "variant_key"]], "gpsea.model.VariantEffect": [[15, 3, 1, "", "CODING_SEQUENCE_VARIANT"], [15, 3, 1, "", "DOWNSTREAM_GENE_VARIANT"], [15, 3, 1, "", "FEATURE_ELONGATION"], [15, 3, 1, "", "FEATURE_TRUNCATION"], [15, 3, 1, "", "FIVE_PRIME_UTR_VARIANT"], [15, 3, 1, "", "FRAMESHIFT_VARIANT"], [15, 3, 1, "", "INCOMPLETE_TERMINAL_CODON_VARIANT"], [15, 3, 1, "", "INFRAME_DELETION"], [15, 3, 1, "", "INFRAME_INSERTION"], [15, 3, 1, "", "INTERGENIC_VARIANT"], [15, 3, 1, "", "INTRON_VARIANT"], [15, 3, 1, "", "MATURE_MIRNA_VARIANT"], [15, 3, 1, "", "MISSENSE_VARIANT"], [15, 3, 1, "", "NMD_TRANSCRIPT_VARIANT"], [15, 3, 1, "", "NON_CODING_TRANSCRIPT_EXON_VARIANT"], [15, 3, 1, "", "NON_CODING_TRANSCRIPT_VARIANT"], [15, 3, 1, "", "PROTEIN_ALTERING_VARIANT"], [15, 3, 1, "", "REGULATORY_REGION_ABLATION"], [15, 3, 1, "", "REGULATORY_REGION_AMPLIFICATION"], [15, 3, 1, "", "REGULATORY_REGION_VARIANT"], [15, 3, 1, "", "SEQUENCE_VARIANT"], [15, 3, 1, "", "SPLICE_ACCEPTOR_VARIANT"], [15, 3, 1, "", "SPLICE_DONOR_5TH_BASE_VARIANT"], [15, 3, 1, "", "SPLICE_DONOR_REGION_VARIANT"], [15, 3, 1, "", "SPLICE_DONOR_VARIANT"], [15, 3, 1, "", "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"], [15, 3, 1, "", "SPLICE_REGION_VARIANT"], [15, 3, 1, "", "START_LOST"], [15, 3, 1, "", "START_RETAINED_VARIANT"], [15, 3, 1, "", "STOP_GAINED"], [15, 3, 1, "", "STOP_LOST"], [15, 3, 1, "", "STOP_RETAINED_VARIANT"], [15, 3, 1, "", "SYNONYMOUS_VARIANT"], [15, 3, 1, "", "TFBS_ABLATION"], [15, 3, 1, "", "TFBS_AMPLIFICATION"], [15, 3, 1, "", "TF_BINDING_SITE_VARIANT"], [15, 3, 1, "", "THREE_PRIME_UTR_VARIANT"], [15, 3, 1, "", "TRANSCRIPT_ABLATION"], [15, 3, 1, "", "TRANSCRIPT_AMPLIFICATION"], [15, 3, 1, "", "UPSTREAM_GENE_VARIANT"], [15, 2, 1, "", "curie"], [15, 4, 1, "", "structural_so_id_to_display"], [15, 4, 1, "", "to_display"]], "gpsea.model.VariantInfo": [[15, 4, 1, "", "has_sv_info"], [15, 4, 1, "", "has_variant_coordinates"], [15, 4, 1, "", "is_structural"], [15, 2, 1, "", "sv_info"], [15, 2, 1, "", "variant_class"], [15, 2, 1, "", "variant_coordinates"], [15, 2, 1, "", "variant_key"]], "gpsea.model.VariantInfoAware": [[15, 2, 1, "", "variant_info"]], "gpsea.model.VitalStatus": [[15, 3, 1, "", "age_of_death"], [15, 2, 1, "", "is_alive"], [15, 2, 1, "", "is_deceased"], [15, 2, 1, "", "is_unknown"], [15, 3, 1, "", "status"]], "gpsea.model.genome": [[16, 1, 1, "", "Contig"], [16, 1, 1, "", "GenomeBuild"], [16, 1, 1, "", "GenomeBuildIdentifier"], [16, 1, 1, "", "GenomicRegion"], [16, 1, 1, "", "Region"], [16, 1, 1, "", "Strand"], [16, 1, 1, "", "Stranded"], [16, 1, 1, "", "Transposable"], [16, 5, 1, "", "transpose_coordinate"]], "gpsea.model.genome.Contig": [[16, 2, 1, "", "genbank_acc"], [16, 2, 1, "", "name"], [16, 2, 1, "", "refseq_name"], [16, 2, 1, "", "ucsc_name"]], "gpsea.model.genome.GenomeBuild": [[16, 4, 1, "", "contig_by_name"], [16, 2, 1, "", "contigs"], [16, 2, 1, "", "genome_build_id"], [16, 2, 1, "", "identifier"]], "gpsea.model.genome.GenomeBuildIdentifier": [[16, 2, 1, "", "identifier"], [16, 2, 1, "", "major_assembly"], [16, 2, 1, "", "patch"]], "gpsea.model.genome.GenomicRegion": [[16, 4, 1, "", "contains"], [16, 2, 1, "", "contig"], [16, 4, 1, "", "distance_to"], [16, 4, 1, "", "end_on_strand"], [16, 4, 1, "", "overlaps_with"], [16, 4, 1, "", "start_on_strand"], [16, 2, 1, "", "strand"], [16, 4, 1, "", "with_strand"]], "gpsea.model.genome.Region": [[16, 4, 1, "", "contains"], [16, 4, 1, "", "contains_pos"], [16, 4, 1, "", "distance_to"], [16, 2, 1, "", "end"], [16, 4, 1, "", "is_empty"], [16, 4, 1, "", "overlaps_with"], [16, 2, 1, "", "start"]], "gpsea.model.genome.Strand": [[16, 3, 1, "", "NEGATIVE"], [16, 3, 1, "", "POSITIVE"], [16, 4, 1, "", "is_negative"], [16, 4, 1, "", "is_positive"], [16, 4, 1, "", "opposite"], [16, 2, 1, "", "symbol"]], "gpsea.model.genome.Stranded": [[16, 2, 1, "", "strand"]], "gpsea.model.genome.Transposable": [[16, 4, 1, "", "to_negative_strand"], [16, 4, 1, "", "to_opposite_strand"], [16, 4, 1, "", "to_positive_strand"], [16, 4, 1, "", "with_strand"]], "gpsea.preprocessing": [[17, 1, 1, "", "CohortCreator"], [17, 1, 1, "", "DefaultImpreciseSvFunctionalAnnotator"], [17, 1, 1, "", "FunctionalAnnotator"], [17, 1, 1, "", "GeneCoordinateService"], [17, 1, 1, "", "ImpreciseSvFunctionalAnnotator"], [17, 1, 1, "", "PatientCreator"], [17, 1, 1, "", "PhenopacketOntologyTermOnsetParser"], [17, 1, 1, "", "PhenopacketPatientCreator"], [17, 1, 1, "", "PhenopacketVariantCoordinateFinder"], [17, 1, 1, "", "PreprocessingValidationResult"], [17, 1, 1, "", "ProtCachingMetadataService"], [17, 1, 1, "", "ProteinAnnotationCache"], [17, 1, 1, "", "ProteinMetadataService"], [17, 1, 1, "", "TranscriptCoordinateService"], [17, 1, 1, "", "UniprotProteinMetadataService"], [17, 1, 1, "", "VVHgvsVariantCoordinateFinder"], [17, 1, 1, "", "VVMultiCoordinateService"], [17, 1, 1, "", "VarCachingFunctionalAnnotator"], [17, 1, 1, "", "VariantAnnotationCache"], [17, 1, 1, "", "VariantCoordinateFinder"], [17, 1, 1, "", "VepFunctionalAnnotator"], [17, 5, 1, "", "configure_caching_cohort_creator"], [17, 5, 1, "", "configure_cohort_creator"], [17, 5, 1, "", "configure_default_protein_metadata_service"], [17, 5, 1, "", "configure_protein_metadata_service"], [17, 5, 1, "", "load_phenopacket_files"], [17, 5, 1, "", "load_phenopacket_folder"], [17, 5, 1, "", "load_phenopackets"]], "gpsea.preprocessing.CohortCreator": [[17, 4, 1, "", "process"]], "gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.FunctionalAnnotator": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.GeneCoordinateService": [[17, 4, 1, "", "fetch_for_gene"]], "gpsea.preprocessing.ImpreciseSvFunctionalAnnotator": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.PatientCreator": [[17, 4, 1, "", "process"]], "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser": [[17, 4, 1, "", "default_parser"], [17, 4, 1, "", "process"]], "gpsea.preprocessing.PhenopacketPatientCreator": [[17, 4, 1, "", "process"]], "gpsea.preprocessing.PhenopacketVariantCoordinateFinder": [[17, 4, 1, "", "find_coordinates"]], "gpsea.preprocessing.PreprocessingValidationResult": [[17, 4, 1, "", "is_ok"], [17, 2, 1, "", "policy"], [17, 4, 1, "", "summarize"]], "gpsea.preprocessing.ProtCachingMetadataService": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.ProteinAnnotationCache": [[17, 4, 1, "", "get_annotations"], [17, 4, 1, "", "store_annotations"]], "gpsea.preprocessing.ProteinMetadataService": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.TranscriptCoordinateService": [[17, 4, 1, "", "fetch"]], "gpsea.preprocessing.UniprotProteinMetadataService": [[17, 4, 1, "", "annotate"], [17, 4, 1, "", "parse_uniprot_json"]], "gpsea.preprocessing.VVHgvsVariantCoordinateFinder": [[17, 4, 1, "", "find_coordinates"]], "gpsea.preprocessing.VVMultiCoordinateService": [[17, 4, 1, "", "fetch"], [17, 4, 1, "", "fetch_for_gene"], [17, 4, 1, "", "get_response"], [17, 4, 1, "", "parse_multiple"], [17, 4, 1, "", "parse_response"]], "gpsea.preprocessing.VarCachingFunctionalAnnotator": [[17, 4, 1, "", "annotate"], [17, 4, 1, "", "with_cache_folder"]], "gpsea.preprocessing.VariantAnnotationCache": [[17, 4, 1, "", "get_annotations"], [17, 4, 1, "", "store_annotations"]], "gpsea.preprocessing.VariantCoordinateFinder": [[17, 4, 1, "", "find_coordinates"]], "gpsea.preprocessing.VepFunctionalAnnotator": [[17, 3, 1, "", "NONCODING_EFFECTS"], [17, 4, 1, "", "annotate"], [17, 4, 1, "", "fetch_response"], [17, 4, 1, "", "format_coordinates_for_vep_query"], [17, 4, 1, "", "process_response"]], "gpsea.util": [[18, 5, 1, "", "open_resource"], [18, 5, 1, "", "open_text_io_handle_for_reading"], [18, 5, 1, "", "open_text_io_handle_for_writing"]], "gpsea.view": [[19, 1, 1, "", "CohortVariantViewer"], [19, 1, 1, "", "CohortViewer"], [19, 1, 1, "", "DiseaseViewer"], [19, 1, 1, "", "Formatter"], [19, 1, 1, "", "GpseaReport"], [19, 1, 1, "", "MtcStatsViewer"], [19, 1, 1, "", "ProteinVariantViewer"], [19, 1, 1, "", "ProteinVisualizable"], [19, 1, 1, "", "ProteinVisualizer"], [19, 1, 1, "", "VariantFormatter"], [19, 1, 1, "", "VariantTranscriptVisualizer"], [19, 5, 1, "", "summarize_hpo_analysis"]], "gpsea.view.CohortVariantViewer": [[19, 4, 1, "", "process"]], "gpsea.view.CohortViewer": [[19, 4, 1, "", "process"]], "gpsea.view.DiseaseViewer": [[19, 4, 1, "", "process"]], "gpsea.view.Formatter": [[19, 4, 1, "", "format_as_string"]], "gpsea.view.GpseaReport": [[19, 4, 1, "", "write"]], "gpsea.view.MtcStatsViewer": [[19, 4, 1, "", "process"]], "gpsea.view.ProteinVariantViewer": [[19, 4, 1, "", "process"]], "gpsea.view.ProteinVisualizable": [[19, 2, 1, "", "marker_counts"], [19, 2, 1, "", "protein_feature_ends"], [19, 2, 1, "", "protein_feature_names"], [19, 2, 1, "", "protein_feature_starts"], [19, 2, 1, "", "protein_feature_types"], [19, 2, 1, "", "protein_id"], [19, 2, 1, "", "protein_length"], [19, 2, 1, "", "protein_metadata"], [19, 2, 1, "", "transcript_coordinates"], [19, 2, 1, "", "transcript_id"], [19, 2, 1, "", "variant_effects"], [19, 2, 1, "", "variant_locations"], [19, 2, 1, "", "variant_locations_counted_absolute"]], "gpsea.view.ProteinVisualizer": [[19, 4, 1, "", "draw_fig"], [19, 4, 1, "", "draw_protein_diagram"]], "gpsea.view.VariantFormatter": [[19, 4, 1, "", "format_as_string"]], "gpsea.view.VariantTranscriptVisualizer": [[19, 4, 1, "", "draw_variants"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "property", "Python property"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"], "5": ["py", "function", "Python function"], "6": ["py", "data", "Python data"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:property", "3": "py:attribute", "4": "py:method", "5": "py:function", "6": "py:data"}, "terms": {"": [4, 6, 7, 9, 10, 11, 12, 14, 15, 16, 17, 22, 26, 27, 28, 30, 32, 34, 35, 36, 44, 45], "0": [1, 2, 3, 6, 8, 10, 15, 16, 17, 19, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 37, 40, 44, 45], "000": 6, "0000002": 31, "0000078": 31, "0000079": 31, "0000080": 31, "0000098": 37, "0000118": [2, 31, 35], "0000119": 31, "0000152": 31, "0000159": 37, "0000223": 31, "0000234": 31, "0000252": 37, "0000256": 37, "0000271": 31, "0000290": 37, "0000306": 37, "0000309": 37, "0000316": 37, "0000356": 31, "0000359": 31, "0000370": 31, "0000377": 37, "0000407": 27, "0000464": 31, "0000478": 31, "0000486": 26, "0000496": 31, "0000504": 31, "0000517": 40, "0000539": 31, "0000553": 31, "0000562": 23, "0000591": 31, "0000598": 31, "0000707": [31, 35], "0000759": 31, "0000769": 31, "0000777": 31, "0000811": 37, "0000818": 31, "0000820": 31, "0000828": 31, "0000834": 31, "0000847": 31, "0000864": 31, "0000924": 31, "0000927": 31, "0000929": 31, "0000951": 31, "0000971": 31, "0001060": 15, "0001115": 35, "0001155": 31, "0001166": [1, 3, 7], "0001167": [23, 26], "0001172": 26, "0001194": 31, "0001197": 31, "0001199": [23, 26], "0001249": 37, "0001250": [7, 8, 15], "0001256": 37, "0001263": 37, "0001311": 31, "0001392": 31, "0001437": 31, "0001438": 31, "0001446": 31, "0001454": 31, "0001507": 31, "0001511": 37, "0001518": 37, "0001537": 6, "0001551": 31, "0001560": 31, "0001566": 15, "0001567": 15, "0001574": [15, 31], "0001575": 15, "0001578": 15, "0001580": 15, "0001583": 15, "0001587": 15, "0001589": 15, "0001595": 31, "0001597": 31, "0001608": 31, "0001619": 15, "0001620": 15, "0001621": 15, "0001623": 15, "0001624": 15, "0001626": [15, 31], "0001627": [15, 27, 31, 37], "0001628": 15, "0001629": [23, 26], "0001630": 15, "0001631": [15, 23, 26], "0001632": 15, "0001671": [23, 26], "0001684": 26, "0001732": 31, "0001743": 31, "0001760": 31, "0001782": 15, "0001787": [15, 31], "0001792": 15, "0001818": 15, "0001819": 15, "0001821": 15, "0001822": 15, "0001871": 31, "0001872": 31, "0001877": 31, "0001881": 31, "0001889": 15, "0001891": 15, "0001892": [15, 31], "0001893": 15, "0001894": 15, "0001895": 15, "0001906": 15, "0001907": 15, "0001928": 31, "0001939": 31, "0001965": 31, "0001977": 31, "0001999": 37, "0002012": [15, 31], "0002019": 15, "0002086": 31, "0002169": 15, "0002170": 15, "0002187": 37, "0002270": 31, "0002339": 35, "0002342": 37, "00024192670136836828": 26, "000242": 26, "0002585": 31, "0002597": 31, "0002664": 31, "0002715": 31, "0002733": 31, "0002793": 31, "0002795": 31, "0002813": 31, "0002814": 31, "0002817": 31, "0002916": 31, "0002926": 31, "0002973": 31, "0002981": 31, "0002984": [23, 26], "0003011": 31, "0003110": 31, "0003111": 31, "0003117": 31, "0003220": 31, "0003254": 31, "0003256": 31, "0003498": 37, "0003549": 31, "0003621": 17, "0003774": 28, "0003839": 31, "0003974": 26, "0004298": 31, "0004312": 31, "0004322": 37, "0004323": 31, "0004328": 31, "0004329": 31, "0004332": 31, "0004337": 31, "0004352": 31, "0004353": 31, "0004356": 31, "0004360": 31, "0004361": 31, "0004370": 31, "0004371": 31, "0004378": 31, "0004404": 31, "0004408": 31, "0004930": 31, "0005120": [23, 26], "0005368": 31, "0005561": 31, "0005922": [23, 26, 37], "0005927": 26, "0006265": 26, "0006476": 31, "0006490": 31, "0006496": [23, 26], "0006500": 31, "0006529": 31, "0006707": 31, "0006889": 37, "0007686": 31, "0008047": 31, "000899": 23, "0008990549794102921": 23, "0009115": [23, 26], "0009124": 31, "0009127": 31, "0009777": [23, 26], "0009778": 26, "0009809": 31, "0009810": 31, "0009815": [23, 26], "0010696": 35, "0010864": 37, "0010876": 31, "0010881": 31, "0010932": 31, "0010935": 31, "0010936": 31, "0010938": 37, "0010948": 31, "0010968": 31, "0010969": 31, "0010974": 31, "0010977": 31, "0010978": 31, "0010987": 31, "0010991": 31, "0011014": 31, "0011017": 31, "0011018": 31, "0011019": 31, "0011024": 31, "0011025": 31, "0011028": 31, "0011032": 31, "0011043": 31, "0011111": 31, "0011121": 31, "0011122": 31, "0011138": 31, "0011277": 31, "0011297": [23, 26], "0011314": 26, "0011342": 37, "0011343": 37, "0011344": 37, "0011409": 31, "0011442": 31, "0011446": 31, "0011620": 31, "0011623": 26, "0011730": 31, "0011732": 31, "0011733": 31, "0011766": 31, "0011767": 31, "0011772": 31, "0011804": 31, "0011805": 31, "0011842": 31, "0011843": 31, "0011844": [23, 26], "0011869": 31, "0011875": 31, "0011884": 31, "0011893": 31, "0011902": 31, "0011994": [23, 26], "0012029": 31, "0012093": 31, "0012099": 31, "0012103": 31, "0012111": 31, "0012129": 31, "0012130": 31, "0012131": 31, "0012135": 31, "0012143": 31, "0012145": 31, "0012210": 27, "0012243": 31, "0012252": 31, "0012261": 31, "0012285": 31, "0012337": 31, "0012338": 31, "0012345": 31, "0012372": [27, 31], "0012373": 31, "0012379": 31, "0012415": 31, "0012443": [8, 27], "0012447": 31, "0012503": 31, "0012535": 31, "0012591": 31, "0012614": 31, "0012632": 31, "0012638": 31, "0012639": 31, "0012640": 31, "0012647": 31, "0012654": 31, "0012680": 31, "0012681": 31, "0012688": 31, "0012700": 31, "0012718": 31, "0012757": 31, "0012769": 31, "0012772": 31, "0020047": 31, "0020054": 31, "0020058": 31, "0020061": 31, "0020155": 31, "0020169": 31, "0025015": 31, "0025021": 31, "0025031": 31, "0025032": 31, "0025033": 31, "0025065": 31, "0025142": 31, "0025155": 31, "0025276": 31, "0025354": 31, "0025427": 31, "0025429": 31, "0025443": 31, "0025454": 31, "0025456": 31, "0025461": 31, "0025463": 31, "0025546": 31, "0025590": 31, "0025640": 31, "0025668": 31, "0025669": 31, "0025688": 31, "0030085": 31, "0030163": 31, "0030272": 31, "0030338": 31, "0030352": 31, "0030453": 31, "0030680": 31, "0030684": 31, "0030687": 31, "0030800": 31, "0030829": 31, "0030860": 31, "0030872": 31, "0030875": 31, "0030878": 31, "0030956": 31, "0030972": 31, "0031071": 31, "0031072": 31, "0031073": 31, "0031093": 31, "0031094": 31, "0031097": 31, "0031099": 31, "0031101": 31, "0031285": 31, "0031331": 31, "0031340": 31, "0031377": 31, "0031383": 31, "0031389": 31, "0031409": 31, "0031411": 31, "0031416": 31, "0031427": 31, "0031476": 31, "0031508": 31, "0031550": 31, "0031602": 31, "0031653": 31, "0031657": 31, "0031685": 31, "0031703": 31, "0031704": 31, "0031818": 31, "0031850": 31, "0031871": 31, "0031884": 31, "0031910": 31, "0031982": 35, "0032120": 31, "0032180": 31, "0032226": 31, "0032243": 31, "0032245": 31, "0032251": 31, "0032314": 31, "0032367": 31, "0032481": 31, "0032485": 31, "0032488": 31, "0032943": 31, "0033012": 31, "0033013": 31, "0033072": 31, "0033127": 31, "0033170": 31, "0033334": 31, "0033335": 31, "0033354": 31, "0033358": 31, "0033796": 31, "0033799": 31, "0034190": 31, "0034200": 31, "0034251": 31, "0034263": 31, "0034370": 31, "0034430": 31, "0034442": 31, "0034482": 31, "0034552": 31, "0034644": 31, "0034684": 31, "0034698": 31, "0034737": 31, "0034858": 31, "0034899": 31, "0034915": 31, "0034916": 31, "0034977": 31, "0037136715160199273": 26, "0040064": 31, "0040068": 31, "0040069": 31, "0040070": 31, "0040084": 31, "0040085": 31, "0040127": 31, "0040172": 31, "0040203": 31, "0040207": 31, "0040214": 31, "0040224": 31, "0040231": 31, "0045026": 31, "0045027": 31, "0045060": [23, 26], "0045081": 31, "005628510156750059": 23, "005806": 26, "005806240832840839": 26, "01": [23, 26, 27, 28, 30, 34, 35, 37, 40], "0100016": 31, "0100022": 31, "0100491": 31, "0100508": 31, "0100530": 31, "0100536": 31, "0100685": 31, "0100705": 31, "0100763": 31, "0100765": 31, "0100766": 31, "0100767": 31, "0100886": 31, "0100887": 31, "012074957610483744": 27, "02560162393963452": 23, "0410008": 31, "0410009": 31, "0410014": 31, "0430071": 31, "04456405819223913": 26, "04502808125400047": 23, "05": [1, 3, 23, 26, 35], "0500012": 31, "0500015": 31, "0500016": 31, "0500017": 31, "0500018": 31, "0500019": 31, "0500020": 31, "0500114": 31, "0500117": 31, "0500166": 31, "0500183": 31, "0500238": 31, "06": [26, 27], "06200425830044376": 28, "06544319142266644": 26, "06932119159387057": 26, "07": [23, 26, 27, 28, 30, 34, 35, 37, 40], "08470708701170182": 26, "0f": 28, "1": [1, 2, 3, 6, 10, 15, 16, 17, 23, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 40, 44, 45], "10": [2, 6, 8, 15, 17, 19, 23, 25, 26, 27, 28, 30, 35, 37], "100": [2, 23, 26, 35], "1000": 15, "1000029": [6, 15, 45], "1001": [15, 32], "1003": 32, "100del": 23, "100dup": [23, 30], "101": 15, "1024del": 23, "106_107insc": [23, 30], "11": [15, 16, 23, 25, 30, 35], "113": 30, "12": [23, 25, 34], "120": [15, 27, 28, 34], "1221c": [23, 34], "123": [8, 10], "129600": 38, "12_114355723_114355723_g_a": 23, "12_114355755_114355756_tg_t": 23, "12_114355784_114355785_ca_c": 23, "12_114356064_114356065_ta_t": 23, "12_114366207_114366208_gc_g": 23, "12_114366241_114366242_ct_c": 23, "12_114366267_114366267_c_a": 23, "12_114366274_114366274_g_t": 23, "12_114366312_114366312_g_a": 23, "12_114366348_114366349_ct_c": 23, "12_114366360_114366360_c_t": 23, "12_114366366_114366366_t_a": 23, "12_114385474_114385474_a_g": 23, "12_114385475_114385475_c_t": 23, "12_114385521_114385521_c_g": 23, "12_114385521_114385521_c_t": [23, 30], "12_114385522_114385522_g_a": [23, 30], "12_114385550_114385550_a_aattattctcag": 23, "12_114385553_114385553_c_a": 23, "12_114385563_114385563_g_a": [23, 30], "12_114394743_114394746_tgtg_t": 23, "12_114394762_114394763_ca_c": 23, "12_114394817_114394817_g_c": 23, "12_114394820_114394820_c_g": 23, "12_114398568_114398568_c_a": 23, "12_114398578_114398579_ca_c": 23, "12_114398602_114398602_t_g": 23, "12_114398626_114398627_cg_c": 23, "12_114398632_114398632_g_a": 23, "12_114398656_114398656_c_cg": [23, 30], "12_114398666_114398667_tg_t": 23, "12_114398675_114398675_g_t": [23, 30], "12_114398682_114398682_c_cg": [23, 30], "12_114398708_114398709_gc_g": 23, "12_114399514_114399514_a_c": [23, 30], "12_114399559_114399559_t_c": 23, "12_114399594_114399594_a_c": 23, "12_114399613_114399613_t_a": 23, "12_114399622_114399622_g_t": 23, "12_114399625_114399629_acatc_a": 23, "12_114399633_114399633_c_g": 23, "12_114401827_114401827_t_a": 23, "12_114401830_114401830_c_t": [23, 30], "12_114401846_114401846_c_g": 23, "12_114401853_114401853_g_t": 23, "12_114401873_114401874_ta_t": 23, "12_114401907_114401907_a_g": 23, "12_114401921_114401921_c_g": 23, "12_114403754_114403754_g_t": 23, "12_114403792_114403792_c_cg": [23, 30], "12_114403798_114403798_g_gc": [23, 30], "12_114403798_114403799_gc_g": 23, "12_114403859_114403859_g_t": 23, "13": [1, 2, 3, 23, 25, 26, 30], "1304del": 23, "1333del": 23, "13654199434471745": 23, "1366c": 23, "14": [23, 25, 26, 30], "142900": 23, "1435th": 45, "145c": 23, "148": 23, "15": [16, 23, 30], "154700": 38, "1554": 34, "156": [23, 26, 30, 34, 40], "16": 23, "161t": 23, "16436": 28, "16th": 17, "17": [23, 26], "18": [23, 26, 34, 40], "1824c": 15, "18262": 28, "18869165": 34, "18869682": 34, "18921399": 34, "19": [23, 26, 27, 30, 34, 45], "194del": 23, "19723": 28, "1_8358231_8358231_t_c": 45, "1d": 19, "1g": 23, "1st": [6, 15, 34], "2": [2, 3, 4, 6, 9, 10, 12, 15, 16, 17, 23, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 44, 45], "20": [2, 6, 15, 23, 25, 26, 27, 28, 30, 35, 45], "2011": 37, "2015": 21, "2018": [27, 34], "2019": 25, "2022": [29, 37], "2024": 27, "205": 15, "206": 15, "207": 28, "21": 26, "211": 23, "215c": 23, "22": [2, 23, 26, 30], "22280": 28, "222g": 23, "223": 15, "224": 15, "22_10001_20000_inv": [6, 15], "23": [23, 26, 31], "238g": [23, 30], "24": 26, "241a": 23, "243": 23, "246_249del": 23, "25": [15, 26, 28], "250": 34, "251": 30, "253a": 17, "253c": 23, "256000": [7, 8], "25_grch37": 18, "262a": 23, "263": 34, "27": [23, 26, 30], "27bp": 15, "28": [23, 26], "281t": 23, "287": 26, "2986": [8, 15, 25], "299": 34, "29th": 17, "2d": 2, "2nd": 6, "2t": 23, "2x2": 4, "2x3": 4, "3": [2, 4, 15, 17, 23, 27, 28, 31, 32, 35, 36], "30": [15, 17, 23, 26, 30], "3000013": 31, "3000036": 31, "3000050": 31, "303": 25, "30552424": 23, "31": [23, 26], "316a": 23, "32": [23, 26, 30], "320": 34, "321681": 15, "321682": 15, "321887": 15, "33": [23, 26], "34": [23, 26], "346": 34, "348081479150901e": 27, "348081479150902e": 27, "353": 23, "356": [30, 34], "36": [23, 26, 30, 35], "3603": [15, 17], "361t": [23, 30], "36303223": 29, "365": 15, "3652": 15, "369": [23, 26, 40], "374del": 23, "38": [23, 30], "38336121": 23, "4": [2, 6, 8, 10, 15, 17, 23, 26, 27, 28, 30, 34, 35], "40": [2, 23, 30, 35], "4000056": 31, "4000183": 31, "400dup": [23, 30], "4065940176561687": 26, "408c": [23, 30], "40c": 23, "41": [23, 26, 30], "416del": 23, "42": [19, 23, 26], "426dup": [23, 30], "43": [23, 26], "4304a": 45, "432292015291845e": 26, "4375": 15, "44": [23, 26], "45": [23, 26], "450": 35, "451c": 23, "456": 10, "456del": 23, "46": [23, 30, 34], "48": [23, 26], "481a": 23, "4870099714553749": 26, "5": [1, 3, 6, 15, 17, 23, 26, 27, 28, 30, 34, 37, 44, 45], "50": [6, 15, 23, 26, 30, 45], "504del": 23, "50bp": 6, "510": 23, "518": [30, 34], "52": 23, "53": [23, 26, 30], "54": [23, 30], "55": [23, 26], "56": [23, 30], "578": 15, "58": 26, "584g": 23, "587c": 23, "59": 26, "5g": 23, "5th": [6, 15, 23], "5x": 27, "6": [15, 23, 26, 27, 28, 29, 30, 32, 35, 45], "60": 23, "6000062": 31, "6000231": 31, "6000489": 31, "6000673": 31, "614": 25, "6190936213143254e": 23, "62": 23, "63": 26, "630": 25, "64": [23, 26, 35], "641del": 23, "65": 26, "658_660del": 23, "664": 25, "668c": [23, 30], "67": 26, "678g": 23, "680_681insctgagaataat": 23, "69": [25, 26], "7": [1, 3, 6, 10, 15, 23, 30, 35], "709c": [23, 30], "71": [23, 26], "710g": [23, 30], "72": 23, "741216622359659": 25, "75": 26, "755": 23, "7703831604944444": 26, "7735491022101784": 23, "78": 26, "781a": 23, "787g": 23, "798del": 23, "8": [8, 15, 17, 18, 23, 25, 26, 30, 34, 35], "80": [26, 34], "833333333333336": 26, "835c": 23, "84": 26, "85": [23, 30], "873c": 23, "880g": 23, "89": 26, "9": [23, 25, 26, 34], "90": [23, 30, 35], "905del": 23, "93": 26, "939del": 23, "94": 23, "95": [23, 35], "97": 26, "9876g": 15, "99": [26, 35], "A": [2, 3, 6, 7, 8, 10, 12, 15, 17, 19, 21, 23, 30, 32, 34, 35, 37, 39, 41, 44], "AND": [6, 27, 45], "AT": 32, "As": [5, 7, 27, 30, 41, 45], "But": 30, "By": [2, 19, 23, 35, 40], "For": [2, 4, 7, 8, 14, 15, 16, 23, 25, 26, 27, 28, 29, 30, 32, 34, 35, 36, 40, 44, 45], "INS": 15, "If": [2, 3, 6, 11, 13, 15, 17, 18, 23, 26, 35, 37], "In": [2, 4, 8, 15, 17, 21, 23, 26, 27, 28, 29, 30, 33, 34, 35, 37, 40, 41, 44], "It": [3, 4, 23, 30, 35, 43], "NO": 7, "NOT": [2, 15, 16, 25, 45], "No": [1, 3, 16, 23, 30, 34, 40], "Not": 15, "OR": [6, 25, 27, 44, 45], "On": [3, 7, 34], "One": [28, 37, 45], "That": 22, "The": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 43, 44, 45], "Then": [15, 22, 23, 34], "There": [15, 23, 24], "These": [6, 15], "To": [17, 22, 23, 26, 27, 34, 35, 45], "_": [27, 28, 34, 40], "__eq__": 6, "__hash__": 6, "__init__": [15, 17], "__repr__": 6, "__str__": 6, "_api": [2, 3], "_cohort": 15, "_io": 17, "_measur": 25, "_missing_implies_phenotype_exclud": 7, "_stat": 3, "_t": 15, "_tempor": 15, "_term_id": 2, "_variant": 44, "a_label": [6, 23, 25, 26, 27, 28, 44], "a_pred": [6, 23, 25, 26, 27, 28, 44], "aa": 6, "aat": 32, "ab": 6, "abbrevi": [19, 35], "abdomen": 31, "abdomin": 31, "abil": 30, "abnorm": [8, 21, 23, 26, 27, 30, 31, 32, 40], "about": [2, 6, 11, 15, 17, 19, 22, 23, 30, 33, 34, 35, 37, 39, 40], "abov": [6, 22, 31, 34, 37, 38], "absenc": [1, 3, 7, 23, 30, 40], "absens": 30, "absent": [23, 26, 30], "absolut": 6, "abstract": [2, 4, 5, 6, 7, 8, 9, 10, 12, 15, 16, 17, 19], "ac": [36, 44], "ac_": 44, "accept": [15, 17], "acceptor": 23, "access": [6, 15, 16, 17, 22, 23, 27, 34, 35, 40], "accommod": 31, "accord": [2, 3, 23, 26, 31], "account": 35, "acetylaspart": 31, "acid": [15, 30, 31, 34], "across": [2, 19, 33, 43], "actg": 32, "activ": [30, 31], "actual": [30, 34], "ad": 37, "adapt": [8, 31, 37], "add": [22, 39], "addit": [4, 22, 23], "addition": 23, "address": 3, "adenosin": 31, "adiponectin": 31, "adipos": 31, "adjac": 16, "adjust": [26, 37], "adnexa": 31, "adren": 31, "adrenocorticotropin": 31, "advanc": 2, "advantag": [23, 26, 35, 40], "affect": [6, 15, 23, 29, 32, 34, 36, 45], "affected_exon": 15, "affects_egfr": 36, "affects_lmna": 36, "after": [1, 3, 17, 22], "ag": [0, 10, 11, 15, 17, 23, 28, 30, 37], "against": 29, "age_of_death": 15, "aii": 28, "aiii": 28, "al": [8, 21, 25, 27, 29, 34, 37], "ala143argfster40": [23, 30], "ala34glyfster27": [23, 30], "ala34profster32": [23, 30], "albumin": 31, "aldosteron": 31, "alel": 44, "align": 15, "aliv": [11, 15], "all": [1, 2, 3, 5, 6, 7, 8, 15, 17, 22, 26, 28, 31, 32, 33, 34, 39, 41, 42, 44, 45], "all_count": [1, 3], "all_diseas": 15, "all_measur": 15, "all_pati": 15, "all_phenotyp": 15, "all_transcript_id": 15, "all_vari": 15, "all_variant_info": 15, "allel": [6, 7, 8, 15, 21, 26, 27, 28, 29, 33, 39, 44, 45], "allele_count": [5, 6, 36], "allelecount": [5, 6], "allianc": 21, "allow": [3, 30, 33, 34, 35, 41, 44], "allow_nan": 14, "alon": 35, "along": [14, 26, 34, 36, 39], "alpha": [1, 3, 26, 31, 35], "alreadi": 34, "also": [15, 31, 34, 39, 40], "alt": [15, 32], "altern": [6, 12, 15, 27, 30, 32, 35, 36], "although": 30, "alwai": [6, 15, 16, 34], "amaz": 34, "amino": [15, 30, 31], "aminoacid": [6, 15, 16, 19, 34], "amniot": 31, "among": [2, 15], "amount": [8, 34], "amyloid": 31, "an": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 44, 45], "analys": [1, 33, 34, 41, 44], "analysi": [0, 15, 17, 19, 21, 24, 29, 33, 34, 36, 37, 38, 40, 41, 43, 44, 45], "analysisresult": [0, 1, 3], "analyz": [0, 8, 10, 19, 23, 25, 27, 28, 30, 41], "anatomi": [23, 34], "ancestor": [7, 23, 32, 40], "andolfo": 34, "aneurysm": 32, "angiotensin": 31, "ani": [2, 5, 6, 8, 14, 15, 17, 26, 27, 30, 34, 35, 36, 37, 38, 45], "ank": [6, 15], "ankyrin": 15, "annot": [2, 6, 7, 11, 15, 17, 19, 23, 26, 30, 32, 34, 35, 40, 45], "annotation_frequency_threshold": [2, 35], "anomali": [27, 37], "anoth": [7, 16, 23, 34], "answer": 6, "anterior": [31, 40], "antimullerian": 31, "anu": 31, "api": [15, 17, 21, 26, 30, 41, 45], "aplasia": [23, 26], "apoptosi": 31, "appear": 31, "appendicular": [23, 26], "appli": [1, 3, 9, 32, 35], "applic": 23, "apply_predicates_on_pati": [1, 3], "approach": [33, 35], "appropri": [23, 24, 30], "ar": [1, 2, 3, 6, 8, 9, 10, 15, 16, 17, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 37, 40, 41, 44, 45], "arachnodactyli": 7, "arbitrari": [14, 16], "areolar": 31, "arg": 14, "arg134profster49": [23, 30], "arg237gln": [23, 30], "arg237pro": 23, "arg237trp": [23, 30], "arg279ter": [23, 30], "arg81trp": 23, "arginin": 45, "argument": [8, 13, 18, 19, 35, 36, 40], "arithmet": 16, "arm": 31, "aromatas": 31, "around": [4, 9, 12, 15], "arrai": [4, 19], "arrang": 31, "arrhythmia": 23, "arriv": 35, "ask": [2, 21], "aspect": [19, 30], "assai": [23, 30], "assembl": 17, "assembli": 16, "assert": [15, 16], "assess": [1, 3, 15, 27, 37], "assign": [1, 3, 5, 6, 7, 8, 10, 15, 26, 27, 37, 38, 39, 41, 44, 45], "assist": 33, "associ": [1, 3, 8, 15, 17, 21, 23, 25, 29, 30, 34, 41], "assum": [15, 16, 17, 25, 35], "assumpt": [35, 40], "atrial": [23, 26, 30, 31], "atrium": [23, 26], "atrophi": 27, "atrophin": 27, "attach": 15, "attain": [1, 3, 28], "attribut": [3, 6, 7, 15, 21], "automat": 27, "autonom": 31, "autosom": [23, 44], "avail": [1, 2, 10, 15, 17, 21, 23, 26, 27, 30, 34, 41, 45], "avoid": [19, 31], "ax": [8, 10, 19, 23, 27, 28, 30, 34], "axi": [27, 28, 31, 36, 39], "b": [6, 15, 16, 35, 44], "b_label": [6, 23, 25, 26, 27, 28, 44], "b_predic": [6, 23, 25, 27, 28, 44], "back": [13, 17, 34], "background": [21, 33], "backup": 15, "bandwidth": 34, "base": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 23, 26, 27, 31, 32, 34, 36, 37, 38, 41, 43], "baseview": 19, "basi": 30, "basic": [15, 16, 34, 45], "batteri": 7, "bb": 6, "becaus": [2, 15, 29, 30, 31, 32, 35, 37], "been": [10, 15, 23, 26, 34, 35], "befor": [15, 45], "behavior": 21, "behind": [23, 40], "being": [1, 2, 3, 12, 16, 17, 19, 23, 30, 35, 37, 41, 45], "belong": [2, 15], "below": [6, 32], "benjamini": [1, 3, 23, 26, 35], "besid": 34, "best": 21, "beta": [31, 34], "better": 45, "between": [3, 8, 10, 11, 15, 16, 19, 21, 23, 25, 26, 27, 28, 30, 32, 35, 37, 43], "beyond": 6, "bia": [15, 34], "biallel": 6, "biallelic_pred": [5, 6, 25, 44], "big": 25, "bin": [1, 3, 5, 6, 23, 27, 35], "bind": 15, "biolog": [15, 16, 27, 34], "biologi": 21, "biomark": 31, "biomed": [23, 34], "biopterin": 31, "birth": [15, 31], "bit": 40, "bleed": 31, "blood": 31, "bodi": 31, "boiler": 34, "boilerpl": 34, "bone": [23, 26, 31], "bonferroni": [23, 35], "bool": [2, 6, 7, 10, 15, 16, 17, 19], "boolean": 15, "borderlin": 37, "both": [1, 4, 15, 17, 23, 37, 38, 41, 44], "bound": [16, 17], "boundari": [15, 16], "box": [8, 27, 30, 34], "bp": [6, 15, 32, 45], "brain": [8, 27], "branch": [22, 35], "break": 15, "breakend": 15, "breakpoint": [6, 15, 17], "breast": 31, "breath": 31, "brief": 21, "bring": [23, 31], "bronchu": 31, "buccal": 31, "bug": 21, "build": [6, 15, 16, 17, 23, 26], "built": 34, "burden": [2, 3, 23, 35], "c": [5, 15, 17, 21, 23, 25, 27, 30, 32, 34, 45], "c17998": 15, "c46112": 15, "c46113": 15, "cach": [13, 17, 34], "cache_dir": 17, "cache_env": [0, 13], "calcium": 31, "calcul": [4, 8, 9, 12, 15, 16, 26, 30], "calf": 31, "call": [14, 15, 31, 34, 35], "callabl": [8, 18], "can": [2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 22, 23, 26, 27, 28, 30, 31, 34, 35, 36, 37, 38, 39, 40, 44, 45], "cannot": [5, 8, 10, 11, 15, 17, 27, 34, 37, 41], "canon": 15, "cap": 35, "capabl": 41, "carboxyl": 31, "cardiac": [23, 26, 30, 31], "cardiomyocyt": 31, "cardiovascular": 31, "carpal": [23, 30], "carri": [27, 29, 34], "cart": 31, "cascad": 31, "case": [2, 8, 15, 17, 23, 26, 27, 30, 34, 40], "cat_id": [1, 5, 8, 10, 25, 27], "catalyt": 30, "cataract": 35, "catecholamin": 31, "categor": [2, 5, 6, 7, 30, 39, 44], "categori": [1, 3, 5, 7, 8, 10, 15, 25, 26, 27, 33, 34, 36, 37, 39], "catheter": 31, "caudat": 35, "caus": [21, 40], "caviti": 31, "ccc": 32, "cct": 15, "cd": [15, 22], "cdna": [15, 23], "cds_end": 15, "cds_start": 15, "cell": [30, 31], "cellular": 31, "censor": [10, 11], "central": 31, "cerebellar": 27, "certain": [6, 15, 30, 35, 39, 45], "certainli": 34, "cg": 32, "chanc": [23, 26, 35], "chang": [6, 15, 27, 33, 34, 45], "change_length": [6, 15, 27, 45], "charact": 15, "character": [15, 23], "characterist": 15, "check": [1, 3, 4, 6, 15, 16, 17, 23, 35, 45], "check_circular": 14, "checker": 34, "checkout": 22, "child": 2, "children": [31, 35], "chin": 37, "choic": [15, 33], "choos": [6, 17, 23, 26, 30, 33], "chosen": [15, 23, 26, 34], "chr1": [15, 16, 32], "chr5": 15, "chrom": [15, 32], "chromosom": [6, 15, 17, 29, 31, 45], "chromosomal_delet": 45, "chronic": 28, "chrx": 16, "cilium": 31, "circul": 31, "cl": [14, 25, 26, 27, 28, 30, 34, 45], "class": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 19, 23, 30, 34, 35, 45], "classifi": 26, "clearanc": 31, "clearli": 45, "click": [15, 34], "clinic": [15, 23, 25, 34, 35, 37, 40], "clinvar": [23, 34], "clone": 22, "cluster": 39, "cm000663": 16, "coagul": 31, "code": [1, 2, 3, 8, 15, 17, 22, 23, 26, 27, 28, 30, 34], "coding_sequence_vari": 15, "codon": [15, 21, 34, 45], "cohort": [0, 2, 3, 6, 7, 8, 10, 15, 17, 19, 21, 33, 36, 41, 42], "cohort_cr": [17, 23, 34, 40], "cohort_nam": 23, "cohort_s": 2, "cohortcr": [0, 17, 34], "cohortvariantview": [0, 19, 23], "cohortview": [0, 19, 23, 30], "coiled_coil": 15, "collect": [2, 5, 6, 7, 9, 12, 15, 17, 21, 23, 34, 40], "color": 8, "column": [1, 2, 3, 8, 10, 15, 28], "com": 22, "combin": [15, 23, 45], "come": [16, 27, 30], "command": 22, "common": [1, 23, 29, 30], "commonli": [16, 35], "compact": [6, 15], "compar": [4, 9, 10, 11, 12, 15, 24, 28, 29, 33, 38, 43, 44], "compare_genotype_vs_phenotyp": [3, 23, 26], "compare_genotype_vs_phenotype_scor": [8, 25, 27], "compare_genotype_vs_surviv": [10, 28], "comparison": [10, 15, 29, 44], "compil": 15, "complain": 17, "complet": [15, 17, 34, 35, 44], "complete_record": 1, "complex": 35, "compon": [27, 45], "composit": [15, 31, 34], "compositional_bia": 15, "compound": [6, 29, 31, 45], "comprehens": [21, 40], "comput": [1, 3, 6, 8, 9, 10, 11, 12, 17, 23, 26, 27, 28, 44], "compute_pv": [4, 9, 12], "compute_surviv": 10, "concentr": 31, "concept": [21, 32, 35], "conceptu": 15, "concern": [21, 27], "concis": 15, "conclus": 35, "condens": 31, "condit": [27, 35], "conduct": [23, 26, 30], "config": 0, "configur": [3, 6, 17, 23], "configure_caching_cohort_cr": [0, 17, 23, 34, 40], "configure_cohort_cr": [0, 17], "configure_default_protein_metadata_servic": [0, 17, 30, 34], "configure_hpo_term_analysi": [1, 3, 23, 26], "configure_ontology_stor": [23, 26, 27, 28, 30, 34, 35, 37, 40], "configure_phenopacket_registri": [23, 34, 40], "configure_protein_metadata_servic": [0, 17, 23], "congenit": [23, 26, 27], "connect": 31, "consequ": 15, "conserv": 15, "consid": [4, 6, 15, 16, 17, 26, 27, 31, 37], "consider": 31, "consist": [2, 15, 16, 34, 35], "consortium": 27, "constitut": 31, "construct": [17, 27, 40], "constructor": [2, 15, 35], "consult": [13, 30], "contain": [1, 2, 8, 15, 16, 17, 19, 23, 28, 31, 34], "contains_po": 16, "contemporari": 30, "content": 34, "context": [2, 21, 27, 35, 44], "contig": [15, 16, 34], "contig_by_nam": [15, 16, 32], "contigu": 16, "conting": [2, 3, 4, 26], "contingency_t": 26, "continuouspartit": [8, 10], "contrast": 37, "contribut": 30, "control": [23, 35], "conveni": [7, 17, 26, 34], "convers": 32, "convert": 17, "coordin": [6, 15, 16, 17, 19, 30, 32], "copi": 29, "cord": 31, "corneal": 31, "corpuscular": 31, "correct": [1, 3, 23, 26, 31, 33], "corrected_pv": [1, 3], "correctli": 17, "correl": [0, 1, 2, 3, 21, 23, 24, 30, 31, 33, 34, 35, 45], "correspon": 28, "correspond": [1, 2, 3, 6, 7, 8, 15, 16, 17, 23, 26, 27, 30, 32, 33, 35, 37, 44, 45], "cortisol": 31, "could": [1, 3, 14], "count": [1, 2, 3, 4, 6, 7, 8, 15, 19, 23, 26, 27, 30, 31, 33, 34, 37, 39, 44], "count_al": 15, "count_deceas": 15, "count_distinct_diseas": 15, "count_distinct_hpo_term": 15, "count_distinct_measur": 15, "count_femal": 15, "count_mal": 15, "count_statist": [3, 26, 35], "count_unique_diseas": 15, "count_unique_measur": 15, "count_unique_phenotyp": 15, "count_unknown_sex": 15, "count_unknown_vital_statu": 15, "count_with_age_of_last_encount": 15, "count_with_disease_onset": 15, "counter": 15, "countingphenotypescor": [1, 8, 27], "counts_fram": 2, "countstatist": [3, 4], "coveni": 15, "cover": [5, 41], "cpd_viewer": 30, "cranial": 31, "creat": [2, 6, 7, 8, 13, 15, 16, 17, 19, 21, 23, 25, 26, 27, 28, 30, 33, 35, 36, 37, 40, 44, 45], "create_variant_from_scratch": 15, "creator": 17, "criteria": [6, 39, 45], "criterion": 6, "cry": 31, "csf": 31, "ct": 15, "culprit": 2, "curat": 23, "curi": [2, 6, 8, 15, 17], "current": [13, 15, 16, 17, 18, 19, 22, 34, 43], "custom": [8, 34, 44], "cut": 40, "cycl": 31, "cyp21a2": 25, "cystein": 15, "cytologi": 31, "cytometri": 31, "d": 15, "dai": [15, 17, 28], "danger": 30, "darksalmon": 8, "data": [1, 2, 3, 4, 8, 10, 15, 16, 17, 19, 21, 23, 25, 26, 27, 30, 33, 35, 39, 40, 45], "data_column": 1, "databas": 17, "datadir": 17, "datafram": [1, 2, 3, 4, 8, 10, 15, 19, 28, 34], "dataset": [23, 26, 30], "days_in_month": 15, "days_in_week": 15, "days_in_year": [15, 28], "de": [8, 33, 42], "death": [10, 11, 15], "decad": 28, "deceas": [11, 15], "decid": [2, 15, 30, 31], "decilit": 15, "decis": 2, "decod": [14, 18, 34], "deem": 31, "deep": 21, "def": [8, 14], "default": [2, 3, 6, 13, 14, 17, 18, 19, 23, 34, 35, 40, 44], "default_cache_path": [0, 13], "default_filt": [2, 26, 35], "default_pars": 17, "defaultimprecisesvfunctionalannot": [0, 17], "defaulttermid": 2, "defect": [23, 26, 27, 30, 32], "defin": [3, 5, 6, 15, 28, 32, 36, 44], "definit": 15, "degre": 37, "dehydr": 34, "del": [6, 15, 32, 45], "delet": [6, 15, 23, 32, 45], "deliveri": 31, "demonstr": [23, 45], "denot": [15, 21, 37], "depend": [1, 23, 24], "deposit": [26, 27], "deriv": 35, "descend": [6, 7, 8, 23, 27, 32, 37, 40], "describ": [8, 15, 17, 22, 25, 26, 27, 28, 30, 35, 37, 40, 44, 45], "descript": [6, 7, 8, 15, 17, 25, 26, 27, 28, 36, 37, 40, 45], "design": [21, 30, 34, 35], "desir": [6, 17, 29, 31, 41], "despit": 23, "detail": [15, 23, 28, 35], "detect": 30, "determin": [6, 15, 17, 27, 35, 37], "develop": [15, 22, 28, 31, 35, 37], "deviat": [21, 26], "devri": [30, 37], "devriesphenotypescor": [1, 8, 27, 37], "df": [15, 34], "diagnos": [6, 7, 11, 15, 23, 30, 38, 39], "diagnosi": [6, 7, 11, 15, 33, 39], "diagnosis_pred": [5, 6, 38], "diagram": [19, 23, 30, 34], "dialog": 34, "dichotom": 26, "dict": [14, 17], "differ": [8, 10, 15, 16, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 41, 43, 44], "differenti": 21, "digest": 31, "digit": [23, 26], "dimension": 15, "dingeman": 37, "diploid": 15, "direct": [7, 15, 23, 35], "directori": [13, 17, 34], "disabl": [27, 35, 37], "discharg": 31, "discoveri": [23, 35], "discret": [3, 4, 5, 41], "diseas": [0, 6, 7, 11, 15, 21, 23, 28, 30, 36, 38, 39, 40, 44], "disease_by_id": 15, "disease_id": 11, "disease_id_queri": 7, "disease_onset": [10, 11], "diseaseanalysi": [1, 3], "diseasepresencepred": [5, 7], "diseaseview": [0, 19], "disord": [23, 30, 34], "displai": [2, 6, 19, 23, 30, 34], "disproportion": 37, "distanc": 16, "distance_to": 16, "distinct": [15, 23, 30], "distribut": [8, 12, 15, 19, 27, 33, 43], "divid": [26, 39], "dl": 15, "dna": [16, 31], "do": [2, 6, 8, 16, 17, 19, 22, 23, 26, 34, 35, 40, 45], "doc": [25, 26, 27, 28, 30, 34, 45], "document": [21, 22, 24, 30, 34, 35], "doe": [2, 11, 13, 15, 17, 32], "domain": [2, 6, 15, 27, 31, 33, 34, 35, 45], "domin": [23, 29, 44], "done": [16, 22, 36, 39, 45], "donor": [15, 23], "dopamin": 31, "doubl": [8, 16], "down": [17, 40], "download": [15, 34], "downloaded_uniprot_json": 34, "downstream": [2, 16, 34, 41], "downstream_gene_vari": [15, 17], "dpi": [27, 28, 34], "dr": 26, "draw": [8, 10, 19, 34], "draw_fig": [19, 34], "draw_protein_diagram": [19, 23, 30], "draw_vari": 19, "drawn": 19, "driven": 31, "drop": 28, "drug": 31, "due": [15, 17], "dump": 14, "dup": 15, "duplic": [15, 17, 32], "durat": 15, "dure": 15, "e": [1, 2, 3, 6, 7, 8, 10, 11, 15, 16, 17, 18, 21, 23, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 40, 44], "each": [1, 2, 3, 6, 7, 8, 10, 15, 17, 19, 21, 23, 26, 27, 28, 29, 30, 33, 35, 37, 41], "ear": 31, "easi": [22, 43], "easiest": 34, "easili": [19, 38], "ectopia": [38, 40], "eff": [27, 45], "effect": [6, 15, 17, 23, 27, 30, 34, 44, 45], "either": [2, 6, 7, 8, 15, 16, 19, 26, 27, 34, 37], "elabor": 45, "electrolyt": 31, "electrophysiologi": 31, "element": [15, 16, 17, 19], "els": 14, "elsewher": [28, 30], "embryon": 31, "empir": 28, "empti": [15, 16, 17], "enabl": 22, "encod": [6, 7, 14, 15, 17, 18, 23, 25, 26, 27, 28, 34, 45], "encount": [11, 15, 23, 30], "end": [6, 15, 16, 17, 23, 28, 32, 34], "end_on_strand": 16, "endocrin": 31, "endpoint": [1, 10], "energi": 31, "enrich": 35, "ensembl": 15, "enst00000123456": 15, "ensur": [18, 44], "ensure_ascii": 14, "enter": 30, "entir": 34, "entiti": [7, 15, 16, 17], "entri": [17, 34, 40], "enum": [15, 16], "enumer": 19, "environ": [13, 19, 22, 30], "enzym": 31, "epiphysi": 31, "equal": [1, 3, 6, 15, 27, 35], "equival": [8, 27], "error": [15, 17, 23, 30, 34, 35], "erythrocyt": 31, "erythroid": 31, "erythropoietin": 31, "et": [8, 21, 25, 27, 29, 34, 37], "etc": [15, 17], "evalu": [6, 21, 26, 27], "even": [3, 31, 34, 35], "ever": 2, "everi": 28, "exact": [3, 4, 6, 8, 15, 17, 21, 23, 24, 27, 29, 30, 33, 35], "exactli": [6, 8, 35], "exampl": [1, 3, 4, 6, 7, 8, 9, 10, 14, 15, 17, 19, 23, 24, 29, 32, 33, 35, 38, 41, 45], "except": [14, 17, 45], "exclud": [2, 5, 7, 15, 16, 23, 26, 36, 40], "excluded_diseas": 15, "excluded_member_count": 15, "excluded_phenotyp": 15, "exclus": [5, 7, 23, 32, 41], "execut": [10, 25, 27, 28], "exemplifi": 30, "exercis": [31, 34], "exhaust": 5, "exibit": 7, "exist": [13, 17, 30, 35], "exon": [6, 15, 23, 28, 34, 45], "exon20": 45, "exon_numb": 6, "exons_effect": 15, "expect": [2, 15, 17, 18, 26, 27, 31, 34, 35, 39], "expenditur": 31, "experiment": 30, "explan": [2, 24, 42], "explicit": [2, 7, 35], "explicitli": [15, 40], "explor": [26, 27, 33, 34, 40], "exploratori": 33, "expos": 26, "express": [10, 17, 26, 31], "extend": 27, "extern": 37, "extract": [15, 17], "extraocular": 31, "extrem": [23, 26, 35], "ey": [27, 31, 40], "f": [8, 21, 28], "face": 31, "fact": [35, 45], "factor": [30, 31, 34, 35, 39], "factori": 2, "fail": [2, 15], "fall": [8, 13], "fallback": [13, 17], "fals": [2, 3, 6, 7, 10, 14, 15, 16, 17, 23, 26, 28, 30, 35], "famili": [15, 23, 35, 38], "far": 27, "farthest": 27, "fascia": 31, "fbn1": [6, 15], "fdr": [26, 35], "fdr_bh": [1, 3, 23, 26, 35], "fdr_by": 35, "fdr_gb": 35, "fdr_tsbh": 35, "fdr_tsbky": 35, "featur": [6, 7, 10, 15, 21, 22, 26, 27, 30, 40, 45], "feature_elong": 15, "feature_id": 6, "feature_trunc": 15, "feature_typ": [6, 15], "featureinfo": [0, 15], "features": 30, "featuretyp": [0, 6, 15], "fecal": 31, "feel": 41, "feenstra": [8, 37], "femal": [15, 23, 30, 43], "fet": [24, 30, 33], "fetal": 31, "fetch": [17, 23, 30, 33], "fetch_for_gen": 17, "fetch_respons": 17, "few": [32, 34, 45], "fh": [18, 19, 25, 26, 27, 28, 30, 45], "fiber": 31, "fibrillin": 15, "fibrinolysi": 31, "fibroblast": 31, "fiction": [6, 44], "field": [11, 15, 29], "fig": [23, 27, 28, 30, 34], "figsiz": [23, 27, 28, 30, 34], "figur": [17, 19, 34], "file": [15, 17, 18, 19, 25, 26, 27, 28, 30, 34, 45], "filter": [2, 3, 15, 23, 26, 31, 32, 33], "filter_method_nam": 2, "final": [26, 40], "find": [3, 16, 17, 23, 26, 34, 35, 39], "find_coordin": 17, "finder": 17, "finger": [15, 23, 26], "fingertip": 34, "finish": 25, "finit": 10, "first": [6, 13, 15, 23, 26, 27, 30, 34, 35, 36, 39], "fisher": [3, 4, 21, 23, 24, 29, 30, 33, 35, 42], "fisher_exact": [4, 26], "fisherexacttest": [3, 4, 26, 35], "fit": 15, "five": 27, "five_prime_utr_vari": [15, 17], "fix": [34, 36], "flexibl": [26, 45], "flip": 16, "float": [1, 2, 3, 4, 8, 9, 10, 12, 15, 17, 26, 27], "flow": 31, "fluid": 31, "focal": 32, "focu": [21, 23], "fold": 15, "folder": [13, 17, 34], "follow": [3, 6, 10, 11, 15, 22, 23, 25, 26, 27, 28, 30, 31, 32, 34, 35, 37, 41, 44, 45], "foot": 31, "for_sampl": 15, "forearm": 31, "forehead": 37, "form": [4, 31, 34], "formal": 30, "format": [7, 15, 16, 17, 19, 30, 34], "format_as_str": 19, "format_coordinates_for_vep_queri": 17, "formatt": [0, 19], "formul": [30, 34], "forward": 16, "found": [15, 17, 23, 27, 30, 34, 35, 37], "four": [30, 34], "fpath_cache_dir": 17, "fpath_cohort": 30, "fpath_cohort_json": [25, 26, 27, 28, 45], "fragment": 15, "frame": [1, 2, 3, 4, 8, 10, 15, 19, 25, 27, 34, 45], "frameshift": [44, 45], "frameshift_vari": [15, 23, 26, 27, 30, 44, 45], "framework": 27, "free": 41, "frequenc": [2, 19, 23, 26, 35], "frequent": [23, 30, 32], "friendli": 2, "from": [2, 5, 6, 8, 10, 11, 12, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32, 33, 35, 36, 37, 38, 40, 41, 43, 44, 45], "from_curi": 40, "from_feature_fram": [15, 34], "from_iso8601_period": 15, "from_map": 15, "from_measurement_id": [8, 25], "from_pati": 15, "from_query_curi": [8, 27], "from_raw_part": 15, "from_str": 15, "from_term": 15, "from_uniprot_json": [15, 34], "from_vcf_liter": [15, 32], "from_vcf_symbol": [15, 32], "fuction": 17, "func": 8, "funcformatt": 28, "function": [4, 6, 7, 8, 9, 12, 15, 17, 18, 23, 26, 27, 30, 31, 34, 40, 44, 45], "functional_annot": 17, "functionalannot": [0, 17], "functionalannotationawar": [0, 15], "further": [23, 27, 40], "furthermor": 34, "fwer": 35, "g": [1, 2, 3, 6, 7, 8, 10, 11, 15, 16, 17, 18, 21, 23, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 40, 44, 45], "ga": 31, "ga4gh": [15, 21, 23, 25, 26, 27, 28, 33, 45], "gain": 23, "galleri": 33, "ganglion": 31, "gastrin": 31, "gastrointestin": 31, "gather": 30, "gb_acc": 16, "gcf_000001405": 18, "ge": [26, 44], "genbank": 16, "genbank_acc": 16, "gene": [6, 15, 17, 23, 26, 27, 29, 30, 34, 36, 40, 45], "gene_coordinate_servic": 17, "gene_id": 15, "gene_nam": 15, "gene_symbol": 15, "genecoordinateservic": [0, 17], "gener": [1, 2, 3, 5, 7, 15, 17, 19, 21, 23, 26, 30, 33, 41], "general_hpo_term": 2, "genet": 21, "genit": 31, "genitalia": 37, "genitourinari": 31, "genom": [6, 15, 17, 18, 21, 23, 30, 32, 34, 45], "genome_build": [17, 23, 30, 34], "genome_build_id": 16, "genomebuild": [15, 16, 17], "genomebuildidentifi": [15, 16], "genomicinterpret": 17, "genomicregion": [15, 16, 34], "genotyp": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 17, 21, 24, 30, 31, 33, 36, 38, 41, 43, 45], "genotype_for_sampl": 15, "genotypepolypred": [1, 2, 3, 5, 6, 8, 10, 41], "gestat": [11, 15, 37], "gestational_dai": 15, "get": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 15, 16, 17, 18, 19, 33, 35], "get_annot": 17, "get_cache_dir_path": [0, 13, 17], "get_categor": [5, 7, 25, 27], "get_categori": 5, "get_category_nam": 5, "get_cds_region": [15, 34], "get_coding_base_count": [15, 34], "get_codon_count": [15, 34], "get_excluded_count": 15, "get_features_variant_overlap": 15, "get_five_prime_utr": [15, 34], "get_hgvs_cdna_by_tx_id": 15, "get_maximum_group_observed_hpo_frequ": 2, "get_number_of_observed_hpo_observ": 2, "get_patient_id": 15, "get_preferred_tx_annot": 15, "get_quest": 6, "get_respons": 17, "get_three_prime_utr": 15, "get_tx_anno_by_tx_id": 15, "get_variant_by_kei": [15, 45], "gg": [15, 17], "git": 22, "github": [22, 41], "give": [6, 34], "given": [2, 6, 7, 10, 15, 17, 18, 19, 37, 40], "gland": 31, "glial": 31, "gln151ter": 23, "gln302argfster92": [23, 30], "gln315argfster79": [23, 30], "gln421ter": 15, "gln456ter": 23, "gln49ly": 23, "global": [21, 37], "globe": [31, 37], "glossari": 33, "glu294ter": [23, 30], "glucagon": 31, "glucocorticoid": 31, "glucos": 31, "gly125alafster25": 23, "gly195ala": 23, "gly80arg": [23, 30], "glycolipid": 31, "glycoprotein": 31, "glycosaminoglycan": 31, "glycosyl": 31, "go": 15, "gonadotropin": 31, "good": [23, 34], "gov": 29, "gp": 23, "gpc": 33, "gpsea": [20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45], "gpsea_cach": [13, 17], "gpsea_cachedir": 13, "gpseajsondecod": [0, 14, 25, 26, 27, 28, 30, 34, 45], "gpseajsonencod": [0, 14, 34], "gpseareport": [0, 19, 30], "granulocytopoiet": 31, "graph": [7, 26], "graphic": [19, 26, 30], "grch37": [16, 17, 34], "grch38": [15, 16, 17, 23, 30, 32, 34], "great": 35, "greater": 35, "grid": [27, 28], "group": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 28, 29, 33, 34, 37, 39, 41, 45], "group1": 27, "group2": 27, "group_label": [5, 23, 25, 26, 27, 28, 36, 38, 40, 43, 44], "growth": [31, 34], "gt": 15, "gt_col": 1, "gt_id_to_nam": [25, 27], "gt_predic": [1, 2, 3, 8, 10, 23, 25, 26, 27, 28, 36, 38, 43, 44], "guid": [21, 23, 34], "h": [15, 35], "h_1": 4, "ha": [1, 2, 3, 6, 7, 8, 10, 11, 15, 16, 23, 26, 27, 30, 31, 34, 37], "had": [2, 23, 30], "hair": 31, "hallmark": 7, "hand": [23, 26, 31, 34, 37], "handl": [5, 18, 19], "happen": 3, "harbor": [27, 36, 44], "has_sv_info": 15, "has_variant_coordin": 15, "hashabl": 15, "have": [2, 8, 15, 26, 34, 35, 37, 44], "head": [25, 27, 28, 31], "health": 21, "hear": 27, "heart": [23, 26, 27, 31, 37], "height": 31, "helic": 15, "help": 23, "hematocrit": 31, "hemizyg": 15, "hemoglobin": 31, "henc": [22, 26], "hepat": 31, "hepatobiliari": 31, "here": [1, 6, 16, 23, 27, 28, 32, 34, 37, 40, 41, 44], "hereditari": 34, "heterozyg": [15, 26, 36, 39], "heterozygot": 29, "heurist": [2, 23, 31, 35], "hgnc": [15, 17], "hgv": [15, 17, 19, 23, 30], "hgvs_cdna": 15, "hgvs_coordinate_find": 17, "hgvsp": 15, "hierarch": 31, "hierarchi": [2, 28, 37, 40], "high": 15, "higher": [26, 27, 37], "highest": 15, "hip": 31, "his1435arg": 45, "his220del": 23, "his445metfster137": 23, "histidin": [15, 45], "histori": 35, "hkd": 30, "hmf01": [23, 26], "hmf02": 2, "hmf03": 2, "hmf05": 2, "hmf07": 2, "hmf08": [2, 23, 26], "hmf09": [23, 26], "ho": 35, "hochberg": [1, 3, 23, 26, 35], "holm": 35, "holt": [23, 30, 45], "homeostasi": 31, "hommel": 35, "homo": 6, "homovanil": 31, "homozygot": 29, "homozygous_altern": 15, "homozygous_refer": 15, "honeydew": 8, "hormon": 31, "how": [16, 22, 23, 24, 34, 40, 45], "howev": [5, 10, 16, 22, 23, 26, 32, 39, 41, 45], "hp": [1, 2, 3, 7, 8, 15, 17, 23, 26, 27, 28, 31, 35, 37, 40], "hpo": [2, 3, 7, 8, 11, 15, 17, 19, 21, 25, 26, 28, 30, 33, 34, 37, 41, 42], "hpo_mtc": 35, "hpo_onset": [10, 11, 28], "hpomtcfilt": [1, 2, 3, 23, 26, 35], "hpopred": [5, 7, 40], "hpotermanalysi": [1, 3, 26, 35, 40], "hpotermanalysisresult": [1, 3, 19], "hpotk": [2, 3, 23, 26, 27, 28, 30, 34, 35, 37, 40], "html": 19, "http": [22, 29], "human": [2, 15, 16, 19, 21, 30, 34, 37], "humor": 31, "hundr": 35, "hypertelor": 37, "hypoplasia": [23, 26, 30], "hypothalamu": 31, "hypothes": [26, 30, 33, 34, 35], "hypothesi": [2, 12, 23, 26, 30, 35], "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 39, 40, 41, 43, 44, 45], "id": [1, 5, 6, 7, 8, 10, 15, 17, 19, 23, 31, 32, 34, 39], "ident": 29, "identifi": [1, 6, 8, 15, 16, 23, 28, 30, 31, 34, 37, 38], "idividu": 26, "idx": 2, "ignor": [9, 17, 34], "ii": 31, "ile106v": 23, "ile227_glu228inst": 23, "ile54thr": 23, "illustr": [23, 26], "img": 34, "immun": 31, "impair": 27, "implement": [4, 6, 10, 14, 17, 24, 26, 29, 33, 34, 37, 43, 44, 45], "implementor": 15, "impli": [7, 26, 32, 35], "implicitli": [32, 40], "import": [4, 6, 8, 15, 16, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 37, 38, 40, 43, 44, 45], "impos": 4, "imposs": [8, 10, 28], "imprecis": [15, 17], "imprecise_sv_functional_annot": 17, "imprecisesvfunctionalannot": [0, 17], "imprecisesvinfo": [0, 15, 17], "includ": [1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 19, 21, 23, 25, 26, 27, 28, 30, 33, 34, 36, 37, 39, 40, 44], "include_computational_tx": 17, "include_ontology_class_onset": 17, "include_patients_with_no_hpo": 15, "include_patients_with_no_vari": 15, "inclus": [6, 39, 45], "incomplete_terminal_codon_vari": 15, "increas": [23, 26, 30], "indel": 15, "indent": [14, 17], "independ": [15, 35], "index": [1, 6, 8, 10, 15, 22, 28, 31, 44], "indic": [1, 3, 15, 44], "indirect": [23, 26, 35], "individu": [1, 2, 3, 5, 6, 7, 8, 10, 11, 12, 15, 21, 23, 25, 26, 27, 28, 29, 30, 32, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45], "infer": 23, "inflammatori": 31, "info": [2, 3, 6, 15, 17, 23, 26, 30, 32, 45], "inform": [6, 10, 15, 19, 21, 23, 30, 33, 34, 35, 37, 41], "infram": 23, "inframe_delet": [15, 23, 30], "inframe_insert": [15, 23, 30], "ingest": 21, "inherit": [25, 35, 39], "inhibin": 31, "initi": [7, 15, 22], "inner": [6, 31], "input": [2, 17, 18, 19, 21, 23, 30, 33], "insert": [15, 17, 23, 32], "insight": [23, 31, 34], "instal": [21, 34], "instanc": [2, 4, 5, 6, 7, 8, 15, 17, 26, 27, 29, 30, 32, 34, 35, 36, 37, 40, 44, 45], "instanti": 34, "instead": [6, 15, 35, 37, 44], "instruct": [21, 25, 26, 27, 28, 45], "insulin": 31, "int": [1, 2, 3, 4, 5, 6, 15, 16, 17, 19], "integ": 15, "integr": [22, 30, 34], "integu": 31, "intellectu": [27, 37], "intend": [8, 15], "inter": [27, 41], "interact": [15, 19, 33], "interest": [6, 7, 15, 17, 23, 26, 30, 31, 33, 35, 44], "intergenic_vari": [15, 17], "intern": 15, "internet": 22, "interpret": [17, 18, 27, 39], "intersect": 16, "interspers": 15, "interv": 16, "intestin": 31, "intracrani": 31, "intraocular": 31, "intrauterin": 37, "introduct": 33, "intron": [15, 23], "intron_vari": [15, 17, 23, 30, 45], "inv": 15, "invers": [6, 15, 45], "investig": [7, 8, 10, 15, 23, 25, 43], "invoc": 22, "involv": [15, 23, 26, 34, 35], "io": [0, 15, 17, 18, 19, 25, 26, 27, 28, 30, 34, 45], "iobas": [15, 18, 19], "ion": [15, 31], "ip3": 15, "ipython": 30, "iqr": 27, "is_al": 15, "is_censor": [10, 28], "is_cod": [15, 34], "is_deceas": 15, "is_empti": 16, "is_femal": 15, "is_filtered_out": 2, "is_frameshift": [26, 44], "is_gest": 15, "is_in_exon3": 28, "is_large_imprecise_sv": 6, "is_mal": 15, "is_missens": [25, 44], "is_neg": 16, "is_observ": 15, "is_ok": 17, "is_pass": 2, "is_posit": 16, "is_postnat": 15, "is_pref": 15, "is_pres": 15, "is_provid": 15, "is_structur": 15, "is_structural_delet": 6, "is_structural_vari": 6, "is_unknown": 15, "islet": 31, "iso8601": 15, "iso8601pt": 15, "isoform": [15, 34], "issu": [2, 15, 17, 21, 23, 34, 41], "item": [2, 3, 5, 17, 19, 32, 37], "iter": [1, 2, 3, 5, 6, 7, 8, 10, 12, 14, 15, 16, 17, 19, 35], "iter_cohort_phenopacket": [23, 34, 40], "its": [7, 11, 15, 19, 27, 32, 40, 41, 45], "j": 3, "jinja2": 19, "joint": 31, "jordan": 27, "json": [14, 15, 17, 25, 26, 27, 28, 30, 45], "jsondecod": 14, "jsonencod": 14, "jt": 29, "judgment": [31, 35], "jupyt": [19, 21, 30], "just": [15, 17, 19, 23, 25, 26, 34, 37], "juvenil": 17, "k": 44, "keep": 7, "kei": [6, 15, 21, 23, 30], "kidnei": [8, 27, 28], "kind": [17, 29, 33, 37], "know": [11, 15, 16, 17, 34], "known": [11, 15, 30, 40], "kwarg": 14, "lab": 25, "label": [6, 8, 11, 15, 19, 25, 28, 31, 34, 38], "label_summari": 15, "labeling_method": 19, "laboratori": 27, "lack": [7, 10, 17, 35], "lactat": 31, "lambda": 28, "langerhan": 31, "larg": [6, 15, 16, 17, 31], "larger": 15, "last": [10, 11, 13, 15, 23, 26, 27, 30], "last_menstrual_period": 15, "later": [25, 26, 27, 28, 33, 45], "latest": 23, "lead": [6, 15, 23, 26, 27, 31, 32, 35, 36, 45], "learn": [23, 26], "least": [2, 6, 17, 23, 26, 27, 35, 41, 44, 45], "leav": [21, 34], "left": 16, "legend": [10, 19, 25], "leigh": 15, "len": [15, 23, 25, 26, 27, 28, 30, 32, 34, 35, 40, 45], "length": [6, 15, 16, 27, 30, 33, 45], "lenient": 17, "lenti": [38, 40], "leptin": 31, "less": [1, 3, 6, 23, 26, 35], "let": [14, 15, 26, 27, 28, 32, 34, 35, 36, 44, 45], "letter": 34, "leu435argfster147": 23, "leu65glnfster10": 23, "leu94arg": 23, "leukocyt": 31, "level": [1, 3, 8, 15, 26, 27, 30, 31, 34, 45], "leverag": [2, 28, 30, 34, 37, 40, 45], "li": [16, 29], "librari": [0, 16, 22, 24, 34], "life": 26, "like": [14, 19, 21, 31, 35], "limb": [23, 26, 31], "limit": [2, 35, 37], "line": [15, 22, 27, 28], "lineag": 31, "link": 39, "lip": 37, "liposaccharid": 31, "list": [6, 7, 8, 14, 15, 23, 26, 31, 37, 40, 41], "list_all_diseas": 15, "list_all_protein": 15, "list_all_vari": 15, "list_measur": 15, "list_present_phenotyp": 15, "liter": [1, 3, 6, 11, 15, 17, 19, 32], "literatur": [6, 23], "liver": [8, 31], "ll": 34, "lmna": 36, "load": [14, 17, 30, 37, 40], "load_minimal_hpo": [23, 26, 27, 28, 30, 34, 35, 37, 40], "load_phenopacket": [0, 17, 23, 34, 40], "load_phenopacket_fil": [0, 17, 34], "load_phenopacket_fold": [0, 17, 34], "loader": 34, "local": [17, 18, 30], "locat": [15, 16, 17, 18, 21, 23, 30, 31, 34, 37, 45], "locu": [15, 44], "lof": 27, "lof_effect": 27, "lof_mut": 27, "log": [12, 28, 30, 42], "logic": [35, 37, 45], "logrank": 12, "logranktest": [10, 12, 28], "loinc": [8, 15, 25], "long": 26, "loss": [15, 27, 44], "lost": 11, "lower": [26, 31, 45], "lump": 44, "ly": 27, "lymph": 31, "lymphat": 31, "lymphocyt": 31, "lys226asn": 23, "lys88ter": 23, "lysosom": 31, "m": [4, 15, 22], "macrocephali": 37, "macroscop": 31, "made": [23, 35], "magic": 30, "mai": [3, 8, 10, 15, 17, 26, 27, 30, 34, 35, 36, 44, 45], "main": [23, 27, 34], "major": [16, 41], "major_assembli": 16, "major_formatt": 28, "major_loc": 28, "make": [6, 30, 35], "male": [15, 23, 30, 43], "mandatori": 15, "mane": [15, 23, 25, 26, 27, 28, 34, 45], "mane_pt_id": 34, "mane_tx_id": 34, "mani": [23, 24, 30, 31, 33, 34, 35, 37, 40, 41, 45], "manifest": [21, 34], "mann": [8, 9, 24, 30, 33, 37, 42], "mannwhitneystatist": [8, 9, 27], "mannwhitneyu": [9, 27], "manual": [15, 26, 30], "map": [2, 15, 17, 19], "marfan": 38, "marker": [19, 31], "marker_count": 19, "marrow": 31, "mass": [8, 15, 25, 27, 31], "match": [6, 8, 11, 27, 39], "matern": 29, "math": 8, "matplotlib": [8, 10, 19, 23, 27, 28, 30, 34], "matrix": [2, 3], "matur": 31, "mature_mirna_vari": 15, "maxim": 41, "maximum": [2, 23, 26, 37], "me": 15, "mean": [15, 26, 27, 31, 35], "meaning": 5, "measur": [0, 8, 15, 23, 24, 27, 30, 31, 33], "measurement_by_id": 15, "measurementphenotypescor": [1, 8, 25, 27], "median": 27, "mediastinum": 31, "medic": [21, 31, 35], "medicin": 21, "meet": [6, 15, 27, 39, 45], "megakaryocyt": 31, "member": [10, 15, 17, 23, 26, 28, 30, 34, 35], "membran": 31, "mendelian": 21, "menstrual": 15, "mental": 31, "mesenteri": 31, "messag": 14, "met": 45, "met74il": 23, "met83phefster6": 23, "meta_label": [15, 34], "metabol": 31, "metabolit": 31, "metadata": [17, 19], "metaphysi": 31, "method": [2, 3, 6, 7, 14, 15, 16, 17, 23, 26, 27, 34, 35], "mhc": 31, "micro": 37, "microcephali": 37, "middl": 31, "midfac": 37, "midpoint": 17, "midwif": 15, "might": [29, 30], "mild": [37, 44], "mim": 23, "miner": 31, "minimalontologi": [2, 3, 7, 8, 11, 17, 19, 40], "minimalterm": 15, "minimum": 2, "mininum": 35, "miss": [10, 11, 17, 41], "missens": [1, 2, 3, 6, 15, 21, 25, 26, 27, 29, 32, 35, 39, 44, 45], "missense_and_exon20": 45, "missense_or_nonsens": 45, "missense_vari": [1, 3, 6, 15, 23, 25, 27, 30, 44, 45], "missing_implies_exclud": 7, "missing_implies_phenotype_exclud": 7, "mitig": [26, 35], "mitochondrion": 31, "mixin": 16, "mnv": 15, "mode": [17, 35, 39], "model": [0, 2, 6, 18, 23, 25, 26, 27, 28, 30, 32, 34, 44, 45], "moder": 37, "modifi": 35, "modul": [0, 15, 16, 26, 27, 30, 34], "moment": 17, "monarch": 22, "mondo": 7, "monoallel": [6, 28], "monoallelic_pred": [5, 6, 23, 26, 27, 28, 44], "monophenotypeanalysisresult": [0, 1, 8, 10], "month": 15, "more": [1, 2, 3, 6, 8, 9, 12, 15, 17, 19, 22, 23, 26, 27, 30, 31, 33, 34, 37, 38, 44, 45], "morpholog": 31, "morphologi": [8, 21, 23, 26, 27, 30, 31, 32, 35, 37, 40], "mortal": 30, "most": [15, 16, 19, 23, 30, 31, 34, 35, 41], "mostli": [15, 41], "motif": [15, 21], "motil": 31, "motor": [23, 31], "movement": 31, "mpl": 28, "mri": 31, "mt": [2, 23, 26, 33], "mtc": [2, 3, 19, 23, 26, 31, 33, 35], "mtc_alpha": [3, 26], "mtc_correct": [1, 3, 26, 35], "mtc_filter": [1, 3, 26, 35], "mtc_filter_nam": 3, "mtc_filter_result": 3, "mtc_issu": 2, "mtc_report": [23, 26], "mtc_viewer": [23, 26], "mtcstatsview": [0, 19, 23, 26], "much": [2, 30, 31, 35, 45], "mucociliari": 31, "mucosa": 31, "mucu": 31, "multi": [15, 45], "multiphenotypeanalysi": [1, 3], "multiphenotypeanalysisresult": [0, 1, 3], "multipl": [1, 2, 3, 23, 26, 31, 33, 45], "multipleloc": 28, "multipli": 35, "muscl": 31, "muscular": 26, "musculatur": 31, "musculoskelet": 31, "must": [2, 3, 5, 6, 7, 8, 10, 15, 17, 22, 26, 27, 30, 34, 38, 41, 44, 45], "mutat": [23, 25, 26, 27, 28, 30, 34, 40, 44, 45], "mutlipl": 35, "myelin": 31, "myeloid": 31, "n": [2, 4, 6, 15, 23, 30, 31, 40], "n_categor": 5, "n_filtered_out": 3, "n_significant_for_alpha": [1, 3], "n_usabl": [1, 2, 3], "nacgtacgtac": 15, "nail": 31, "name": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 15, 16, 17, 18, 25, 27, 28, 30, 34, 38, 40, 44], "nan": [1, 3, 8, 9, 10, 25, 27], "nanogram": 15, "nasal": 31, "natur": 15, "nc_000001": 16, "ncbi": [23, 29], "ncit": 15, "ndarrai": 19, "neck": 31, "need": [15, 17, 23, 26, 28, 33, 34, 35, 40, 44], "neg": [6, 15, 16, 17, 32], "neoplasm": 31, "neopterin": 31, "neq": 44, "nerv": 31, "nervou": [31, 32, 35], "net": 15, "network": 34, "neuron": 31, "never": [16, 35], "new": 19, "next": [23, 34, 36, 45], "ng": 15, "nih": 29, "nippl": 31, "nlm": 29, "nm_000500": 25, "nm_001042681": [27, 45], "nm_002834": 17, "nm_003361": 28, "nm_005912": 17, "nm_013275": 45, "nm_123": 6, "nm_1234": [6, 44], "nm_123456": [1, 3, 6, 15], "nm_170707": 15, "nm_181486": [23, 26, 30, 34], "nmd_transcript_vari": 15, "no_cal": 15, "no_genotype_has_more_than_one_hpo": 2, "node": 31, "nomin": [1, 3, 23, 26, 35], "non": [2, 3, 6, 10, 15, 17, 23, 26, 27, 35, 45], "non_coding_transcript_exon_vari": [15, 17], "non_coding_transcript_vari": [15, 17], "non_frameshift_del": 45, "non_frameshift_effect": 45, "non_frameshift_pred": 45, "non_specified_term": 2, "noncoding_effect": 17, "none": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 19, 23, 27, 28, 34, 35, 37, 41, 44], "nonfaci": 37, "nons": 29, "nonsens": [2, 3, 6, 25, 26, 29, 35, 45], "normal": 21, "nose": 37, "notat": [15, 32], "note": [2, 3, 7, 13, 15, 16, 23, 26, 34, 37, 38, 43, 44, 45], "notebook": [19, 21, 30], "notepad": 17, "noth": 45, "novel": 15, "now": [15, 23, 25, 26, 27, 28, 34, 35, 40, 44], "np_": 23, "np_000129": 15, "np_001027558": 17, "np_001027559": 15, "np_037407": 17, "np_852259": [23, 30, 34], "nuclear": 15, "nucleobas": 31, "nucleotid": [15, 23, 32, 45], "nucleu": 35, "nul": 15, "null": 35, "number": [1, 2, 3, 4, 5, 6, 8, 15, 16, 23, 26, 27, 28, 31, 35, 37], "numer": [15, 30], "o": [14, 17], "obj": 14, "object": [1, 2, 3, 6, 8, 10, 14, 15, 16, 17, 19, 34], "object_hook": 14, "observ": [2, 8, 15, 21, 23, 26, 30, 40], "observablefeatur": 15, "obtain": [15, 17, 23, 34, 35, 37], "obvious": 30, "occipitofrontali": 31, "occur": [15, 23, 27, 30, 34], "occurr": 23, "oddsratio": 26, "odontoid": 31, "off": [41, 45], "offer": [24, 30, 35, 37, 42, 45], "offlin": 17, "often": 15, "ok": [2, 17], "oldest": 35, "omim": [7, 8, 38], "omit": [2, 23, 26, 35, 38, 41, 43, 44], "onc": [15, 26, 34], "one": [2, 5, 6, 7, 8, 15, 17, 22, 23, 26, 27, 28, 29, 30, 31, 34, 36, 37, 41, 44], "one_genotype_has_zero_hpo_observ": 2, "ones": 17, "onli": [2, 5, 6, 7, 15, 17, 23, 26, 29, 30, 35, 40], "onlin": 22, "only_hgv": 19, "onset": [10, 11, 15, 17, 23, 28, 30, 31, 32], "onsetawar": 15, "onto": 19, "ontologi": [2, 3, 7, 15, 17, 21, 23, 32, 34, 37], "ontology_class": 17, "ontologyclass": 17, "oocyt": 31, "open": [18, 25, 26, 27, 28, 30, 34, 41, 45], "open_phenopacket_stor": [23, 34, 40], "open_resourc": [0, 18], "open_text_io_handle_for_read": [0, 18], "open_text_io_handle_for_writ": [0, 18], "oper": [6, 15, 45], "oppos": 15, "opposit": 16, "option": [2, 6, 7, 15, 17, 22, 23, 34, 35, 40, 44], "oram": [23, 30, 45], "order": [2, 15, 23, 26, 30, 34, 44], "organ": [15, 27, 31], "orgogozo": 21, "origin": 37, "orthogon": 39, "osmol": 31, "osteocalcin": 31, "other": [2, 15, 16, 17, 19, 21, 23, 25, 26, 28, 29, 34, 35, 36, 37, 39, 44], "otherwis": [6, 7, 10, 15, 37], "our": [23, 24, 26, 28, 31, 35, 37, 41], "out": [2, 3, 5, 16, 17, 23, 26, 27, 28, 32, 34, 35], "outcom": [1, 3], "outer": [6, 31], "output": [17, 18, 19], "over": 15, "overal": [2, 35], "overlap": [3, 6, 15, 16, 19, 23, 28, 45], "overlapping_exon": 15, "overlaps_with": [15, 16], "overlaps_with_fifth_aa": 6, "overlaps_with_first_20": 6, "overload": [15, 45], "overrepres": 15, "overview": [23, 24, 30], "own": 16, "p": [1, 2, 3, 4, 7, 8, 9, 12, 15, 19, 21, 23, 26, 30, 34, 35, 40, 45], "p10y": 15, "p10y4m2d": 15, "p13": [16, 17], "p13_assembly_report": 18, "p22w3d": 15, "p2w6d": 15, "p_valu": [26, 27], "packag": [18, 20, 21, 22, 35], "page": [15, 23, 30, 33, 41], "pair": [3, 4, 6, 12, 15, 32], "pancrea": 31, "pancreat": 31, "panda": [2, 15, 34], "param": [6, 15, 16, 17, 18], "paramet": [1, 2, 3, 5, 6, 7, 8, 10, 12, 14, 15, 16, 17, 18, 19], "parametr": 27, "parathyroid": 31, "parent": [3, 17, 35, 37], "pars": [15, 17], "parse_multipl": 17, "parse_respons": 17, "parse_uniprot_json": 17, "parser": 17, "part": [1, 15, 19, 34, 37], "particular": 30, "partit": [1, 5, 6, 7, 8, 10, 25, 36, 41, 43], "pass": [2, 6, 14, 15, 32, 35], "past": 35, "patch": [8, 16], "patern": 29, "path": [13, 15, 17, 18, 19, 23, 26, 33, 34, 40], "pathogen": [23, 34, 45], "patient": [0, 1, 2, 3, 5, 6, 7, 8, 10, 15, 17, 19, 21, 23, 26, 27, 34, 35, 36, 40, 41], "patient_1": 10, "patient_2": 10, "patient_3": 10, "patient_4": 10, "patient_cr": 17, "patient_id": [10, 15, 25, 27, 28], "patientcategori": [5, 7], "patientcr": [0, 17], "pattern": 31, "payload": 17, "pcat": [1, 23, 26, 35], "pd": [15, 34], "pediatr": 17, "pehnotyp": 2, "peptid": 31, "per": 15, "percent": [23, 26], "percentag": 35, "perform": [4, 15, 17, 21, 23, 26, 27, 29, 30, 33, 34, 35], "perifollicular": 31, "period": 15, "peripher": 31, "peritoneum": 31, "permiss": [17, 34], "peroxisom": 31, "persist": [25, 26, 27, 28, 33, 45], "ph": [30, 31], "ph_col": 1, "ph_predic": 2, "phagocytosi": 31, "phe168leufster6": 23, "pheno_pred": [1, 3, 23, 26, 40], "pheno_scor": [8, 25, 27, 37], "phenopacket": [15, 17, 21, 23, 25, 26, 27, 28, 30, 33, 40, 45], "phenopacket1": 34, "phenopacket2": 34, "phenopacket_registri": 23, "phenopacketontologytermonsetpars": [0, 17], "phenopacketpatientcr": [0, 17], "phenopacketvariantcoordinatefind": [0, 17], "phenotyp": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 17, 21, 24, 28, 30, 31, 33, 37, 39, 41, 45], "phenotype_by_id": 15, "phenotype_cr": 17, "phenotype_scor": [8, 27], "phenotypecategor": [5, 7], "phenotypemtcfilt": [1, 2, 3, 23, 35], "phenotypemtcissu": [1, 2], "phenotypemtcresult": [1, 2, 3], "phenotypepolypred": [1, 2, 3, 5, 7, 41], "phenotypescor": [1, 8, 9], "phenotypescoreanalysi": [1, 8, 25, 27, 28], "phenotypescoreanalysisresult": [1, 8], "phenotypescorestatist": [8, 9], "phenotypic_abnorm": 2, "phosphat": 31, "physician": 15, "physiolog": 31, "physiologi": [21, 31, 32], "pick": 26, "pickl": 17, "piec": 15, "piezo1": 34, "pineal": 31, "pinna": 37, "pip": 22, "pituitari": 31, "place": [21, 34], "placent": 31, "placenta": 31, "plan": 30, "plasma": [8, 15, 25, 27], "plate": 34, "platelet": 31, "platform": 18, "platysma": 31, "pld1": 30, "pleas": [30, 41], "plot": [8, 10, 19, 28, 33], "plot_boxplot": [8, 27], "plot_kaplan_meier_curv": [10, 28], "plt": [19, 23, 27, 28, 30, 34], "plu": [6, 15], "pm": [23, 34], "pm_servic": 30, "pmid": 23, "pmid_22034507_aii_1": 28, "pmid_22034507_aii_2": 28, "pmid_22034507_aii_3": 28, "pmid_22034507_aii_5": 28, "pmid_22034507_aiii_4": 28, "pmid_27087320_subject_1": 27, "pmid_27087320_subject_10": 27, "pmid_27087320_subject_2": 27, "pmid_29330883_subj": 34, "pmid_29330883_subject_1": 27, "pmid_29330883_subject_2": 27, "pmid_30968594_individual_10": 25, "pmid_30968594_individual_11": 25, "pmid_30968594_individual_12": 25, "pmid_30968594_individual_13": 25, "pmid_30968594_individual_14": 25, "png": 34, "po": [15, 16, 28, 32], "point": [15, 17, 27, 34, 37], "point_mut": 27, "point_mutation_effect": 27, "polar": [34, 35], "polici": [17, 23, 34], "polypred": [1, 5, 6, 7], "pore": 34, "port": 16, "posit": [3, 6, 15, 16, 17, 23, 26, 30, 32, 35], "posixpath": 13, "possibl": [2, 3, 5, 8, 29, 30, 34, 43], "possible_result": 2, "possibli": 39, "posterior": [31, 35], "postnat": [11, 15], "postnatal_dai": 15, "postnatal_year": 15, "potassium": 30, "potenti": [27, 33], "power": [33, 35, 41], "pp": 17, "pp_dir": 34, "pp_directori": 17, "pp_file": 17, "pp_file_path": 34, "ppktstore": [23, 34, 40], "practic": 29, "pre": [2, 3], "precis": 21, "precursor": 31, "predic": [1, 2, 3, 4, 8, 10, 33, 36, 38, 43], "predict": [6, 15, 23, 26, 27, 30, 34, 44, 45], "predictor": [17, 34], "prefer": [15, 30], "preimplant": 31, "prematur": 21, "prenat": 31, "prepar": [3, 6, 7, 15, 17, 25, 26, 27, 28, 34, 36, 45], "prepare_hpo_terms_of_interest": [5, 7], "prepare_predicates_for_terms_of_interest": [5, 7, 23, 26, 40], "preprocess": [0, 15, 23, 30, 34, 40], "preprocessingvalidationresult": [0, 17, 34], "preproprotein": 15, "prerequisit": 37, "presenc": [1, 3, 6, 7, 15, 23, 26, 27, 30, 34, 35, 36, 39, 40, 45], "present": [1, 3, 7, 8, 15, 16, 19, 23, 26, 27, 30, 37, 38, 44], "present_diseas": 15, "present_phenotyp": 15, "present_phenotype_categor": 7, "present_phenotype_categori": 7, "pressur": 31, "pretti": 19, "prevent": [2, 3, 45], "previou": [35, 44], "previous": 26, "primari": [15, 31, 45], "principl": 29, "print": [15, 17, 34], "pro139glnfster11": 23, "pro14thr": [23, 30], "pro85thr": 23, "probabl": [26, 35], "problem": 35, "proce": 17, "procedur": [23, 26, 31, 33], "process": [17, 19, 23, 26, 30, 34, 40], "process_respons": 17, "produc": [1, 2, 4, 5, 7, 8, 30], "product": 19, "profound": 37, "programmat": [6, 17], "programmaticali": 34, "project": 15, "prolifer": 31, "prong": [26, 41], "pronounc": 21, "propagatingphenotypepred": 7, "properti": [1, 2, 3, 4, 5, 7, 8, 10, 15, 16, 17, 19], "proport": 35, "protcachingmetadataservic": [0, 17], "protein": [6, 15, 16, 17, 19, 21, 31, 33, 45], "protein_altering_vari": 15, "protein_cach": 17, "protein_effect_coordin": 15, "protein_effect_end": 15, "protein_effect_loc": 15, "protein_effect_start": 15, "protein_featur": [6, 15, 34], "protein_feature_end": 19, "protein_feature_nam": 19, "protein_feature_start": 19, "protein_feature_typ": [6, 19], "protein_id": [15, 17, 19, 34], "protein_length": [15, 19, 34], "protein_meta": [15, 19, 23, 30, 34], "protein_metadata": [6, 19, 30], "protein_sourc": 17, "proteinannotationcach": [0, 17], "proteinfeatur": [0, 15], "proteinmetadata": [0, 6, 15, 17, 19, 23, 34], "proteinmetadataservic": [0, 17, 34], "proteinpred": 41, "proteinvariantview": [0, 19, 30], "proteinvisu": [0, 19, 23, 30, 34], "proteinvisualiz": [0, 19, 34], "provid": [1, 2, 3, 6, 7, 8, 10, 11, 12, 15, 16, 17, 19, 21, 23, 24, 27, 30, 33, 35, 37, 40, 41, 44], "proxi": 37, "pscore": [1, 25, 27, 37], "pt_id": 30, "public": 37, "publish": [22, 40], "pubm": 29, "pulmonari": 31, "pupillari": 31, "purin": 31, "purpos": [2, 25, 26, 28, 30, 34, 35, 45], "put": [15, 25, 27, 28], "putamen": 35, "pval": [1, 3, 8, 10, 25, 27, 28], "pval_kind": [1, 3], "pvalu": 27, "pvi": [19, 34], "px": 30, "px_id": 23, "py": 15, "pydoc": 34, "pypi": 22, "pyplot": [23, 27, 28, 30, 34], "pyrimidin": 31, "pytest": 22, "python": [4, 14, 21, 22, 26, 30, 34, 35, 45], "python3": 22, "q": [23, 34], "q1": 27, "q3": 27, "q99593": 34, "qc_result": 34, "qual": [15, 32], "qualnam": [15, 16], "quartil": 27, "queri": [7, 8, 15, 17, 27, 34, 40], "question": [6, 21, 24, 45], "r": 27, "radiu": [23, 26, 30], "rais": [5, 14, 15, 16, 17], "random": [4, 15], "random_se": 19, "rang": [2, 15, 17, 27, 37], "rank": [9, 12, 27, 28, 30, 42], "rare": [0, 2, 23, 34, 40], "rate": [23, 31, 35], "rather": 31, "ratio": 31, "re": 15, "reach": 17, "read": [18, 19, 21, 45], "readabl": [15, 19], "reader": 34, "readi": [15, 23], "readili": 34, "real": [25, 26], "realiz": 35, "realli": 34, "reason": [2, 23, 26, 31, 34], "receiv": 23, "receptor": 34, "recess": 44, "recommend": [2, 6, 15, 21, 23, 26, 30, 34, 35, 40], "record": [15, 23, 30, 40], "red": [27, 31], "redox": 31, "reduc": [2, 23, 26, 34, 35], "redund": 35, "ref": [6, 15, 19, 32], "ref_length": [6, 27], "refer": [6, 15, 21, 27, 31, 33, 34, 37], "reflect": 41, "reflex": 31, "refract": 31, "refseq": [15, 16, 17, 34], "refseq_nam": 16, "regard": [2, 10, 15, 19, 23, 30], "regardless": 15, "region": [6, 15, 16, 19, 23, 30, 32, 34, 45], "registri": [23, 34, 40], "regul": [30, 31], "regulatory_region_abl": 15, "regulatory_region_amplif": 15, "regulatory_region_vari": 15, "rel": [6, 37], "relat": 35, "relationship": [21, 26], "releas": [23, 26, 27, 28, 30, 31, 34, 35, 37, 40], "relev": [2, 15, 23, 27, 34], "remot": [17, 34], "remov": [6, 31, 32, 45], "renal": [27, 28], "renin": 31, "repair": 31, "repeat": 15, "replac": 45, "report": [1, 3, 8, 10, 15, 17, 19, 21, 23, 25, 26, 27, 28, 30, 40], "repositori": 22, "repres": [1, 2, 3, 5, 6, 7, 8, 10, 15, 16, 17, 19, 21, 27, 34, 35], "represent": [15, 17], "reproduct": 31, "request": 17, "requir": [1, 4, 10, 15, 22, 23, 41], "requisit": 34, "rere": [27, 34, 45], "rere_mane_tx_id": 45, "residu": [6, 15, 30, 34], "resolut": 15, "resourc": [6, 15, 17, 18, 34], "respect": [3, 10, 15, 26, 32, 33, 34, 44, 45], "respir": 31, "respiratori": 31, "respons": [17, 27, 31, 34], "rest": [15, 17, 25, 31], "restrict": 29, "result": [1, 2, 3, 8, 10, 15, 17, 19, 21, 23, 25, 26, 27, 28, 30, 31, 34, 35, 40, 41, 45], "retain": 35, "retainin": 23, "reticulocyt": 31, "retriev": [15, 16, 17], "return": [2, 3, 4, 5, 6, 7, 8, 11, 14, 15, 16, 17, 18, 19, 35, 41], "reus": 44, "revers": 16, "right": [16, 19], "risk": 26, "rna": 16, "root": [2, 31, 35], "row": [1, 2, 3, 23], "rule": [5, 11, 23, 26, 30, 33, 40, 45], "run": [17, 25, 27, 28, 34], "runner": 17, "runonlin": 22, "rust": 15, "sai": 35, "salient": [19, 30], "salivari": 31, "same": [2, 3, 6, 12, 15, 16, 23, 26, 27, 31, 32, 34, 35, 37, 44], "same_count_as_the_only_child": 2, "sampl": [12, 15, 23], "sample_id": 15, "samplelabel": [0, 15], "sapien": 6, "save": 34, "savefig": 34, "scalp": 31, "scenario": 5, "schema": [15, 17, 19, 26, 34], "scienc": 6, "scientif": 30, "scipi": [4, 9, 12, 26, 27], "scipyfisherexact": 3, "sclera": 31, "score": [1, 8, 9, 12, 24, 30, 33, 42], "score_analysi": [25, 27], "score_statist": [8, 25, 27], "scorer": [8, 27], "screenshot": 34, "search": [17, 23, 31, 34, 41], "sebac": 31, "second": [6, 17, 30], "secondari": 15, "secret": 31, "section": [2, 3, 6, 7, 8, 15, 17, 23, 25, 26, 27, 28, 30, 35, 44, 45], "secundum": [23, 26, 30], "sediment": 31, "see": [2, 3, 6, 7, 8, 9, 10, 15, 19, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 44, 45], "seek": 39, "seem": 41, "seen": [15, 27, 35], "segment": [15, 31, 40], "segreg": 31, "seizur": [23, 32], "select": [2, 6, 10, 23, 26, 27], "self": [14, 16], "sens": [30, 31, 35], "sensat": 31, "sensibl": 30, "sensori": 31, "sensorineur": 27, "separ": [14, 26, 42], "septal": [23, 26, 30, 32], "septum": [23, 26, 32], "sequenc": [1, 2, 3, 4, 5, 6, 7, 9, 12, 15, 16, 17, 19, 33, 34], "sequence_vari": 15, "ser196ter": 23, "ser261ci": [23, 30], "ser36thrfster25": [23, 30], "serial": [25, 26, 27, 28, 45], "serializ": 14, "serum": [8, 15, 25, 27, 31], "serv": 41, "servic": 17, "set": [2, 8, 13, 15, 23, 26, 27, 28, 35, 36, 40, 44], "setup": [26, 30, 35], "sever": [3, 5, 15, 23, 25, 26, 27, 30, 32, 34, 35, 37, 42, 44, 45], "sex": [0, 6, 7, 8, 15, 23, 30, 31, 33, 39], "sex_pred": [5, 6, 43], "sh": 35, "shape": 37, "sharpei": 31, "shelf": [27, 41, 45], "shift": 45, "ship": 34, "short": [15, 23, 26, 30, 37], "shortcut": 15, "shorter": [6, 26], "should": [2, 3, 6, 7, 13, 15, 16, 17, 19, 23, 25, 27, 34], "show": [15, 19, 25, 26, 27, 28, 30, 31, 32, 34, 35, 40, 41, 45], "shown": [33, 34], "sidak": 35, "side": [4, 12, 27], "sign": [15, 16, 23, 25, 26, 27], "signal": [31, 35], "signific": [1, 3, 15, 26, 27, 31, 35, 37], "significant_phenotype_indic": [1, 3], "significantli": [23, 26, 27], "sime": 35, "similar": [15, 27, 44], "similarli": [10, 40, 44], "simpl": [6, 22, 29, 32, 34, 37, 45], "simplest": 35, "simpli": [2, 35], "simplifi": [23, 26], "sinc": [3, 6, 15, 27], "sine": 15, "singl": [1, 2, 15, 23, 36, 45], "situ": 31, "size": [2, 15, 16, 30, 31], "skelet": 31, "skeleton": [23, 26], "skin": [8, 31], "skinfold": 31, "skip": [2, 23, 26, 31], "skipkei": 14, "skipping_general_term": 2, "skipping_non_phenotype_term": 2, "skipping_since_one_genotype_had_zero_observ": 2, "skull": 31, "slice": 16, "small": [15, 32, 35, 37], "smell": 31, "snv": [15, 32, 45], "so": [6, 15, 27, 34, 35, 45], "so_term": 15, "softwar": 24, "sole": 26, "solut": 34, "somat": 31, "some": [1, 4, 17, 21, 22, 30, 34, 35, 36, 41], "some_cell_has_greater_than_one_count": 2, "sometim": [36, 44, 45], "sort": [15, 17], "sort_index": [25, 27, 28], "sort_kei": 14, "sound": [31, 40], "sourc": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 45], "span": [6, 15, 16, 31, 32, 34], "specif": [3, 6, 15, 17, 21, 23, 27, 28, 30, 31, 34, 35, 40], "specifi": 2, "specified_term": 35, "specifiedtermsmtcfilt": [1, 2, 35], "specifytermsstrategi": 26, "spell": 32, "spinal": 31, "spleen": 31, "splice": [15, 23], "splice_acceptor_vari": [15, 17, 23, 30], "splice_donor_5th_base_vari": [15, 17, 23, 30], "splice_donor_region_vari": 15, "splice_donor_vari": [15, 17, 23, 30], "splice_polypyrimidine_tract_vari": [15, 17], "splice_region_vari": [15, 23, 30], "spuriou": 35, "st1": 2, "stabil": [15, 31], "stage": [15, 28], "stalk": 31, "standalon": 19, "standard": [15, 33], "start": [6, 15, 16, 17, 19, 27, 30, 31, 34, 44], "start_lost": [15, 27], "start_on_strand": 16, "start_retained_vari": 15, "stat": [3, 8, 10, 25, 26, 27, 28, 35], "state": [15, 32], "static": [2, 6, 8, 14, 15, 17, 35], "statist": [1, 3, 4, 8, 9, 10, 12, 21, 23, 31, 33, 35, 37, 41], "statsmodel": 35, "statu": [0, 2, 11, 15, 23, 30], "statur": 37, "stdout": 17, "step": [22, 23, 26, 33, 34, 39], "stimul": 31, "stomatocytosi": 34, "stool": 31, "stop": [23, 31], "stop_gain": [6, 15, 23, 27, 30, 45], "stop_lost": 15, "stop_retained_vari": [15, 23, 30], "storag": 17, "store": [1, 8, 15, 17, 19, 23, 26, 27, 28, 30, 34, 35, 37, 40], "store_annot": 17, "str": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 32, 34], "strabismu": 26, "strand": [6, 15, 16, 34], "strategi": [2, 19, 26, 31], "stress": 31, "strict": 17, "string": [8, 15, 17, 19, 31], "stringio": 17, "stromal": 31, "strongli": [6, 15], "structur": [6, 10, 15, 26, 27, 30, 31, 32, 35, 37, 45], "structural_defect": 27, "structural_so_id_to_displai": 15, "structural_typ": [6, 15, 45], "structural_vari": 6, "student": 15, "studi": [11, 21, 28], "stump": 31, "sub": [15, 26, 34], "subclass": [6, 14], "subgroup": 15, "subject": [15, 27, 34, 40], "submodul": 20, "subpackag": 20, "subplot": [23, 27, 28, 30, 34], "subsect": 15, "subsequ": [26, 34], "subunit": 31, "successfulli": [23, 30], "suffix": [17, 34], "suggest": 30, "suitabl": 15, "sum": [27, 37, 44], "sum_": 44, "summar": [5, 15, 17, 19, 32, 34], "summari": [5, 17, 33, 34], "summarize_group": [5, 6], "summarize_hpo_analysi": [0, 19, 23, 26], "summary_df": [23, 26], "suox": 29, "super": 14, "supercoil": 15, "suppli": 15, "support": [6, 14, 15, 16, 21, 29, 45], "supports_shap": 4, "suppos": 14, "suppresor": 15, "surf1": [6, 15], "surf2": 6, "surfac": 31, "surviv": [1, 10, 11, 12, 24, 33, 35, 36, 42], "survival_analysi": 28, "survival_statist": 28, "survivalanalysi": [1, 10, 28], "survivalanalysisresult": [1, 10], "survivalmetr": 12, "survivalstatist": [10, 12], "sv": [6, 15, 17, 25], "sv_delet": 32, "sv_info": 15, "svart": 16, "svlen": [15, 32], "svtype": [15, 32], "sweat": 31, "switch": 22, "symbol": [6, 15, 16, 23, 32, 34, 36], "symptom": [15, 23, 25, 26, 27, 31], "synapt": 31, "syndrom": [15, 23, 30, 38, 45], "synonym": 45, "synonymous_vari": [15, 45], "system": [15, 16, 31, 32, 35, 37], "t": [9, 15, 17, 19, 23, 25, 30, 32], "tabl": [4, 19, 23, 26, 30, 31, 32, 33, 35, 44], "tail": 26, "take": [4, 6, 8, 17, 23, 26, 34, 35, 36, 38, 40], "tall": 37, "tandem": 15, "target": [3, 6, 7, 11, 30, 34, 36, 38, 45], "tast": 31, "taxon": 6, "tbx5": [30, 34, 40], "tbx5_gpsea_with_uniprot_domain": 34, "technic": 21, "tediou": [40, 45], "tedium": 40, "temperatur": 31, "templat": 19, "tempor": [1, 15, 28], "ten": [15, 35], "tend": 15, "term": [1, 2, 3, 7, 8, 11, 15, 17, 19, 21, 23, 25, 26, 27, 28, 30, 32, 33, 37, 40, 41], "term_frequency_threshold": [2, 26, 35], "term_id": [8, 11, 15, 25, 28], "term_id_to_ag": 17, "term_onset_pars": 17, "termid": [2, 3, 6, 7, 8, 11, 15, 40], "termin": [15, 21], "terms_to_test": [2, 35], "test": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 16, 17, 19, 21, 23, 24, 29, 31, 33, 37, 39, 40, 41, 42, 45], "test_nam": 15, "test_result": 15, "test_term_id": 15, "test_uniprot_json": 15, "testabl": 30, "testosteron": [8, 15, 25, 27], "text": 18, "textio": [5, 17, 18], "textiowrapp": [17, 18], "tf_binding_site_vari": 15, "tfbs_ablat": 15, "tfbs_amplif": 15, "th": 3, "than": [1, 2, 3, 6, 15, 23, 26, 27, 31], "thank": 26, "thei": [16, 21, 24, 26, 27, 31, 35, 45], "them": 30, "themselv": 16, "therebi": 2, "therefor": [2, 3, 6, 26, 31, 35, 45], "thi": [1, 2, 3, 6, 7, 8, 11, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 39, 40, 43, 44, 45], "thick": 31, "thin": 4, "thing": 30, "think": 35, "third": 27, "thorac": 31, "those": [36, 44], "thr161pro": 23, "thr223met": [23, 30], "thr72ly": 23, "three": [6, 15, 29, 35, 44], "three_prime_utr_vari": [15, 17], "threshold": [2, 6, 23, 26, 35], "thrombocyt": 31, "thrombosi": 31, "through": [15, 34], "thu": [1, 3, 15, 30, 35, 37], "thumb": [5, 23, 26, 30, 45], "thymu": 31, "thyroid": 31, "tick": 28, "ticker": 28, "tight_layout": 34, "tild": 45, "time": [3, 11, 15, 17, 22, 26, 28, 34, 35], "timelin": [0, 11, 15], "timeout": 17, "tissu": 31, "tl": 26, "to_displai": 15, "to_negative_strand": 16, "to_opposite_strand": 16, "to_positive_strand": 16, "to_str": 15, "todo": [19, 25, 29, 34, 39, 41, 42], "togeth": [15, 25, 27, 28], "tonsil": 31, "too": 31, "toolkit": [8, 17, 23, 34, 37], "top": [3, 7, 8, 15, 23, 27, 30, 31, 34], "top_phenotype_count": 19, "top_variant_count": 19, "total": [1, 3, 15, 23, 26, 27, 30, 35, 37], "total_patient_count": 15, "total_test": [1, 3, 23, 26], "track": 7, "tracker": [21, 41], "tract": 31, "trans_id": 15, "transcript": [1, 3, 6, 15, 17, 19, 23, 25, 26, 27, 28, 30, 33, 44, 45], "transcript_abl": [15, 27], "transcript_amplif": 15, "transcript_coordin": 19, "transcript_id": [6, 15, 19, 23, 30], "transcriptannot": [0, 15, 17], "transcriptcoordin": [0, 15, 17, 19, 23, 34], "transcriptcoordinateservic": [0, 17], "transcriptinfoawar": [0, 15, 17], "transform": [17, 34], "transit": 16, "translat": 15, "transloc": [6, 15], "transmiss": 31, "transpos": [15, 16], "transpose_coordin": [15, 16], "trascript": 23, "tri": 17, "triphalang": [23, 26, 30], "triphosph": 31, "trp121gly": [23, 30], "true": [2, 6, 7, 10, 14, 15, 16, 17, 19, 23, 26, 28, 30, 33, 34, 35, 40, 45], "truli": 30, "truncat": 23, "try": [13, 14, 16, 17], "tsv": 18, "ttest_ind": 9, "tteststatist": [8, 9, 25], "tupl": [3, 6, 8, 15, 17, 23, 34, 35, 36, 40], "turn": [17, 34], "tutori": [21, 26, 33], "twice": 35, "two": [1, 3, 4, 6, 8, 12, 15, 16, 18, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 41, 44], "tx": [17, 19, 45], "tx_annot": 15, "tx_coordin": [19, 23, 30, 34], "tx_id": [6, 15, 17, 19, 23, 25, 26, 27, 28, 30, 44, 45], "tx_servic": 30, "txc_servic": [23, 34], "type": [1, 2, 3, 6, 7, 8, 14, 15, 16, 17, 19, 21, 33, 34, 35, 45], "typeerror": 14, "typic": [3, 15, 26, 39, 41], "tyr136ter": [23, 30], "tyr291ter": [23, 30], "tyr342thrfster52": [23, 30], "tyr407ter": [23, 34], "u": [8, 9, 23, 24, 26, 30, 33, 34, 37, 44, 45], "ucsc": 16, "ucsc_nam": 16, "ucum": 15, "umbil": 31, "umbilicu": 31, "umod": 28, "unambigu": 38, "unavail": 15, "under": [17, 23, 34, 35], "underli": 45, "undoubtedli": 34, "uniform": 6, "uninterest": 31, "uniprot": [15, 17, 30], "uniprot_json": [15, 34], "uniprotproteinmetadataservic": [0, 15, 17], "uniqu": [2, 3, 15, 23, 30], "unit": [15, 16, 22, 30], "unknown": [6, 15, 23, 30], "unknown_sex": [15, 43], "unless": [7, 23, 34, 35, 40], "unlik": [31, 35], "unnecessari": 31, "unsur": 30, "until": [11, 28], "untransl": [15, 34], "up": [23, 27, 35, 37, 40], "upper": [23, 26, 31], "upstream": 16, "upstream_gene_vari": [15, 17], "urat": 31, "uri": 15, "urin": 31, "urinari": 31, "urobilinogen": 31, "us": [1, 2, 3, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 39, 40, 41, 44, 45], "usabl": [1, 3], "usag": [6, 7, 9, 19, 45], "use_al": 35, "usealltermsmtcfilt": [1, 2, 35], "user": [15, 19, 21, 23, 26, 30, 31, 34], "usual": [6, 15, 26, 31, 41], "utf": [17, 18], "util": [0, 6, 26], "utr": [15, 34], "uvea": 31, "v": [21, 25, 27, 28, 35], "v2024": [23, 26, 27, 28, 30, 34, 35, 37, 40], "vagin": 31, "val": 2, "val153serfster21": 23, "val214glyfster12": 23, "val263met": [23, 30], "val267trpfster127": [23, 30], "valid": [17, 19, 23, 30, 35], "validation_polici": 17, "validation_runn": 17, "validationrunn": 17, "valu": [1, 2, 3, 4, 8, 9, 10, 12, 15, 16, 17, 19, 23, 24, 26, 27, 28, 33, 35], "valueerror": [5, 15, 16, 17], "valv": 31, "varcachingfunctionalannot": [0, 17], "vari": [6, 26], "variabl": [4, 7, 8, 13, 15, 26, 30, 39], "variable_nam": [7, 8], "variant": [0, 1, 3, 4, 6, 15, 17, 19, 21, 25, 26, 27, 28, 32, 33, 35, 36, 39, 41], "variant_class": [6, 15, 45], "variant_coordin": [15, 17], "variant_effect": [6, 15, 19, 23, 25, 26, 27, 44, 45], "variant_effect_count_by_tx": 15, "variant_fallback": 17, "variant_info": 15, "variant_kei": [6, 15, 17], "variant_key_of_interest": 45, "variant_loc": 19, "variant_locations_counted_absolut": 19, "variantannotationcach": [0, 17], "variantclass": [0, 6, 15, 45], "variantcoordin": [0, 15, 17, 32], "variantcoordinatefind": [0, 17], "varianteffect": [0, 6, 15, 17, 19, 23, 25, 26, 27, 44, 45], "variantformatt": [0, 19], "variantinfo": [0, 15], "variantinfoawar": [0, 15], "variantpred": [5, 6, 23, 25, 26, 27, 28, 36, 39, 41, 44, 45], "varianttranscriptproteinartist": 19, "varianttranscriptvisu": [0, 19], "variou": [16, 37], "vascular": 31, "vasculatur": 31, "vc": [15, 17], "vcf": 15, "vcv000522858": 45, "ventricular": [23, 26, 30, 31, 32], "vep": 17, "vepfunctionalannot": [0, 17], "veri": [2, 44], "verify_term_id": 2, "version": [4, 23, 26, 27, 37, 40], "versu": 28, "vessel": 31, "via": [7, 14, 17, 19, 34], "view": [0, 21, 23, 26, 30, 34], "viewer": [23, 30], "virtual": 22, "vision": 31, "visual": [19, 23, 27, 30, 31, 34], "vital": [11, 15, 23, 30], "vital_statu": 15, "vitalstatu": [0, 15], "vitamin": 31, "voic": 31, "vol": 15, "volum": [8, 15, 25, 27, 31], "vri": [8, 33, 42], "vvhgvsvariantcoordinatefind": [0, 17], "vvmulticoordinateservic": [0, 17, 23, 30, 34], "w": [15, 17], "wa": [1, 2, 3, 5, 7, 15, 19, 23, 25, 26, 27, 28, 30, 35, 37, 40, 45], "wai": [23, 24, 30, 34], "waist": 31, "wall": 31, "want": [2, 8, 26, 27, 34, 35, 36, 44, 45], "warn": [17, 23, 34], "we": [2, 3, 6, 8, 11, 15, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45], "websit": 34, "week": 15, "weight": 31, "well": [6, 7, 15, 30, 34, 38], "were": [1, 3, 17, 19, 23, 26, 27, 30, 34, 40], "what": [26, 39], "whatsoev": 6, "when": [2, 7, 15, 28, 34, 35, 40], "where": [1, 2, 3, 15, 17, 23, 37, 44], "wherea": 30, "whether": [7, 8, 15, 21, 26, 30], "which": [1, 2, 4, 5, 7, 15, 23, 26, 30, 33, 34, 37, 44, 45], "while": [4, 15, 26, 29, 36, 41, 44], "whisker": 27, "whitnei": [8, 9, 24, 30, 33, 37, 42], "who": [7, 23, 27, 29, 44], "whose": [15, 23, 26, 27, 40], "why": 2, "widespread": 30, "wikipedia": 30, "wilcoxon": 27, "wise": [23, 35], "with_cache_fold": 17, "with_strand": 16, "within": [15, 23, 26, 27, 30], "without": [6, 11, 26, 30], "word": [21, 31], "wordsmith": 25, "work": [2, 13, 17, 26, 34], "workflow": 30, "worth": 2, "would": [2, 8, 15, 21, 26, 27, 29, 30, 35, 37, 45], "wrap": [8, 15, 26, 34, 45], "wrap_scoring_funct": 8, "wrapper": [4, 9, 12, 18], "write": [17, 18, 19], "written": 19, "wwox": 40, "x": [27, 28], "x_1000001_1000027_": 15, "x_1000001_1000027_taaaaaaaaaaaaaaaaaaaaaaaaaa_t": 15, "x_12345_12345_c_g": [6, 15], "xaxi": 28, "xlabel": 28, "xm_": 17, "xu": 25, "y": [15, 27, 28], "ye": [1, 3, 7, 40], "year": [15, 17, 28], "yet": 15, "yield": 35, "ylabel": [27, 28], "ylim": 27, "you": [14, 15, 16, 30, 34, 35], "your": [16, 22, 34], "zero": [2, 6, 16, 32, 36, 37], "zero_vs_on": 6, "zero_vs_one_vs_two": 6, "zinc": 15, "zinc_fing": 15, "\u03b1": 15, "\u03c72": 4}, "titles": ["gpsea package", "gpsea.analysis package", "gpsea.analysis.mtc_filter package", "gpsea.analysis.pcats package", "gpsea.analysis.pcats.stats package", "gpsea.analysis.predicate package", "gpsea.analysis.predicate.genotype package", "gpsea.analysis.predicate.phenotype package", "gpsea.analysis.pscore package", "gpsea.analysis.pscore.stats package", "gpsea.analysis.temporal package", "gpsea.analysis.temporal.endpoint package", "gpsea.analysis.temporal.stats package", "gpsea.config module", "gpsea.io module", "gpsea.model package", "gpsea.model.genome package", "gpsea.preprocessing package", "gpsea.util module", "gpsea.view package", "API reference", "GPSEA", "Installation", "Tutorial", "Statistical analyses", "Compare measurement values", "Compare genotype and phenotype groups", "Compare phenotype scores in genotype groups", "Survival analysis", "Genotype-Phenotype Correlations in Autosomal Recessive Diseases", "Cohort exploratory analysis", "General HPO terms", "Glossary", "User guide", "Input data", "Multiple-testing correction", "Group by allele count", "De Vries Score", "Group by diagnosis", "Genotype Predicates", "HPO predicate", "Predicates", "Phenotype Predicates", "Group by sex", "Group by variant category", "Variant Predicates"], "titleterms": {"2x2": 35, "2x3": 35, "The": [23, 37], "abnorm": [35, 37], "across": 30, "all": [23, 35, 40], "allel": [23, 32, 36], "altern": 34, "an": 32, "analys": 24, "analysi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 25, 26, 27, 28, 30, 35], "api": [20, 34], "ar": 35, "associ": 26, "autosom": 29, "background": 35, "biallel": [36, 44], "block": 45, "build": 45, "categori": 44, "chang": 32, "child": 35, "choos": [34, 35], "code": 37, "cohort": [23, 25, 26, 27, 28, 30, 34, 35, 40, 45], "compar": [25, 26, 27, 36], "complex": 45, "condit": 45, "config": 13, "configur": [25, 26, 27, 28, 34], "congenit": 37, "content": [24, 33, 39, 41, 42], "control": 34, "coordin": 34, "correct": 35, "correl": 29, "count": [35, 36], "creat": 34, "creator": 34, "curv": 28, "custom": 26, "data": [28, 34], "de": 37, "default": 26, "delai": 37, "descend": 35, "development": 37, "diagnosi": 38, "diseas": 29, "distribut": [23, 30, 34], "domain": 30, "dump": 34, "dysmorph": 37, "egfr": 36, "endpoint": [11, 28], "enter": 34, "exact": 26, "exampl": [25, 26, 27, 28, 34, 36, 40, 44], "exclud": 35, "explor": [23, 30], "exploratori": 30, "facial": 37, "featur": [34, 37], "feedback": 21, "fet": 26, "fetch": 34, "filter": 35, "final": [25, 27, 28, 37], "fisher": 26, "frameshift": [23, 26], "from": 34, "ga4gh": 34, "galleri": 41, "gener": [31, 35], "genom": 16, "genotyp": [6, 23, 25, 26, 27, 28, 29, 34, 35, 39, 44], "get": 34, "glossari": 32, "gpsea": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 35], "group": [26, 27, 35, 36, 38, 43, 44], "growth": 37, "guid": 33, "ha": 35, "hmf01": 35, "hmf02": 35, "hmf03": 35, "hmf05": 35, "hmf06": 35, "hmf07": 35, "hmf08": 35, "hmf09": 35, "hpo": [23, 27, 31, 35, 40], "ident": 35, "implement": 35, "individu": 36, "input": 34, "instal": 22, "interact": 30, "interest": 34, "invert": 45, "io": 14, "json": 34, "kaplan": 28, "later": 34, "latest": 22, "length": 32, "level": 35, "literatur": 21, "load": [23, 25, 26, 27, 28, 34, 45], "mann": 27, "manual": 34, "measur": 25, "meier": 28, "missens": 23, "missing_implies_phenotype_exclud": 40, "model": [15, 16], "modul": [13, 14, 18], "monoallel": [36, 44], "more": [35, 41], "mt": 35, "mtc_filter": 2, "multipl": 35, "mutat": 36, "need": 41, "neither": 35, "non": 37, "nor": 35, "observ": 35, "occur": 35, "one": 35, "onset": 37, "packag": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19], "pars": 34, "partit": 44, "path": 32, "pcat": [3, 4], "persist": 34, "phenopacket": 34, "phenotyp": [7, 23, 25, 26, 27, 29, 34, 35, 40, 42], "plot": [23, 30, 34], "postnat": 37, "power": 30, "predic": [5, 6, 7, 23, 25, 26, 27, 28, 39, 40, 41, 42, 44, 45], "prenat": 37, "prepar": 23, "preprocess": 17, "procedur": 35, "protein": [23, 30, 34], "provid": 34, "pscore": [8, 9], "qualiti": 34, "rare": 35, "raw": 28, "recess": 29, "refer": [20, 32], "releas": 22, "respect": [23, 30], "rest": [26, 34], "retard": 37, "rule": 32, "run": 22, "score": [25, 27, 37], "scorer": 37, "section": 37, "sequenc": [23, 30], "sex": 43, "shape": 4, "show": 23, "showcas": 34, "skip": 35, "sourc": 34, "specifi": 35, "stabl": 22, "standard": 34, "stat": [4, 9, 12], "statist": [24, 25, 26, 27, 28, 30], "strategi": 35, "submodul": 0, "subpackag": [0, 1, 3, 5, 8, 10, 15], "summar": 23, "summari": [23, 30], "support": 4, "surviv": 28, "tbx5": [23, 26], "tempor": [10, 11, 12], "term": [31, 35], "test": [22, 25, 26, 27, 28, 30, 35], "than": 35, "transcript": 34, "true": 32, "tutori": [23, 29], "type": 30, "u": 27, "underpow": 35, "uniprot": 34, "us": 37, "user": 33, "util": 18, "v": [23, 26], "valid": 34, "valu": 25, "variant": [23, 30, 34, 44, 45], "veri": 35, "view": 19, "vri": 37, "which": 35, "whitnei": 27}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"API reference": [[20, null]], "Alternative phenopacket sources": [[34, "alternative-phenopacket-sources"]], "Analysis": [[25, "analysis"], [26, "analysis"], [27, "analysis"], [28, "analysis"]], "Background": [[35, "background"]], "Biallelic predicate": [[44, "biallelic-predicate"]], "Biallelic predicate genotype groups": [[44, "id8"]], "Building blocks": [[45, "building-blocks"]], "Categories": [[44, "categories"]], "Change length of an allele": [[32, "change-length-of-an-allele"]], "Choose the transcript": [[34, "choose-the-transcript"]], "Choose the transcript and protein of interest": [[34, "choose-the-transcript-and-protein-of-interest"]], "Cohort exploratory analysis": [[30, null]], "Cohort summary": [[30, "cohort-summary"]], "Compare genotype and phenotype groups": [[26, null]], "Compare measurement values": [[25, null]], "Compare phenotype scores in genotype groups": [[27, null]], "Compare the individuals with EGFR mutation": [[36, "compare-the-individuals-with-egfr-mutation"]], "Compare the individuals with monoallelic and biallelic mutations": [[36, "compare-the-individuals-with-monoallelic-and-biallelic-mutations"]], "Complex conditions": [[45, "complex-conditions"]], "Configure a cohort creator": [[34, "configure-a-cohort-creator"]], "Configure analysis": [[25, "configure-analysis"], [26, "configure-analysis"], [27, "configure-analysis"], [28, "configure-analysis"]], "Contents:": [[24, null], [33, null], [39, null], [41, null], [42, null]], "Create a cohort from GA4GH phenopackets": [[34, "create-a-cohort-from-ga4gh-phenopackets"]], "Custom analysis": [[26, "custom-analysis"]], "De Vries Score": [[37, null]], "Default analysis": [[26, "default-analysis"]], "Developmental delay": [[37, "developmental-delay"]], "Distribution of variants across protein domains": [[30, "distribution-of-variants-across-protein-domains"]], "Enter features manually": [[34, "enter-features-manually"]], "Example": [[34, "example"], [34, "id4"], [40, "example"], [44, "example"], [44, "id5"], [44, "id6"]], "Example analysis": [[25, "example-analysis"], [26, "example-analysis"], [27, "example-analysis"], [28, "example-analysis"]], "Examples": [[36, "examples"]], "Exploration": [[30, "exploration"]], "Explore cohort": [[23, "explore-cohort"]], "Facial dysmorphic features": [[37, "facial-dysmorphic-features"]], "Feedback": [[21, "feedback"]], "Fetch data from UniProt REST API": [[34, "fetch-data-from-uniprot-rest-api"]], "Fetch protein data": [[34, "fetch-protein-data"]], "Fetch transcript coordinates from Variant Validator REST API": [[34, "fetch-transcript-coordinates-from-variant-validator-rest-api"]], "Final analysis": [[25, "final-analysis"], [27, "final-analysis"], [28, "final-analysis"]], "Final score": [[37, "final-score"]], "Fisher exact test (FET)": [[26, "fisher-exact-test-fet"]], "GPSEA": [[21, null]], "Gallery": [[41, "gallery"]], "General HPO terms": [[31, null]], "Genotype Predicates": [[39, null]], "Genotype phenotype associations": [[26, "genotype-phenotype-associations"]], "Genotype predicate": [[25, "genotype-predicate"], [26, "genotype-predicate"], [27, "genotype-predicate"], [28, "genotype-predicate"]], "Genotype-Phenotype Correlations in Autosomal Recessive Diseases": [[29, null]], "Get the transcript data": [[34, "get-the-transcript-data"]], "Glossary": [[32, null]], "Group by allele count": [[36, null]], "Group by diagnosis": [[38, null]], "Group by sex": [[43, null]], "Group by variant category": [[44, null]], "HMF01 - Skip terms that occur very rarely": [[35, "hmf01-skip-terms-that-occur-very-rarely"]], "HMF02 - Skip terms if no genotype group has more than one count": [[35, "hmf02-skip-terms-if-no-genotype-group-has-more-than-one-count"]], "HMF03 - Skip terms if all counts are identical to counts for a child term": [[35, "hmf03-skip-terms-if-all-counts-are-identical-to-counts-for-a-child-term"]], "HMF05 - Skip term if one of the genotype groups has neither observed nor excluded observations": [[35, "hmf05-skip-term-if-one-of-the-genotype-groups-has-neither-observed-nor-excluded-observations"]], "HMF06 - Skip term if underpowered for 2x2 or 2x3 analysis": [[35, "hmf06-skip-term-if-underpowered-for-2x2-or-2x3-analysis"]], "HMF07 - Skipping terms that are not descendents of Phenotypic abnormality": [[35, "hmf07-skipping-terms-that-are-not-descendents-of-phenotypic-abnormality"]], "HMF08 - Skipping \u201cgeneral\u201d level terms": [[35, "hmf08-skipping-general-level-terms"]], "HMF09 - Skipping terms that are rare on the cohort level": [[35, "hmf09-skipping-terms-that-are-rare-on-the-cohort-level"]], "HPO MT filter strategy": [[35, "hpo-mt-filter-strategy"]], "HPO predicate": [[40, null]], "Implementation in GPSEA": [[35, "implementation-in-gpsea"]], "Input data": [[34, null]], "Installation": [[22, null]], "Interactive exploration": [[30, "interactive-exploration"]], "Inverting conditions": [[45, "inverting-conditions"]], "Kaplan-Meier curves": [[28, "kaplan-meier-curves"]], "Latest release": [[22, "latest-release"]], "Length of the reference allele": [[32, "length-of-the-reference-allele"]], "Literature": [[21, "literature"]], "Load HPO": [[23, "load-hpo"], [27, "load-hpo"]], "Load cohort": [[25, "load-cohort"], [26, "load-cohort"], [27, "load-cohort"], [28, "load-cohort"], [45, "load-cohort"]], "Load phenopackets": [[34, "load-phenopackets"]], "MT filters: Choosing which terms to test": [[35, "mt-filters-choosing-which-terms-to-test"]], "Mann-Whitney U Test": [[27, "mann-whitney-u-test"]], "Monoallelic predicate": [[44, "monoallelic-predicate"]], "Monoallelic predicate genotype groups": [[44, "id7"]], "Multiple-testing correction": [[35, null]], "Multiple-testing correction procedures": [[35, "multiple-testing-correction-procedures"]], "Need more?": [[41, "need-more"]], "Non-facial dysmorphism and congenital abnormalities": [[37, "non-facial-dysmorphism-and-congenital-abnormalities"]], "Parse UniProt JSON dump": [[34, "parse-uniprot-json-dump"]], "Partitions": [[44, "partitions"]], "Persist the cohort for later": [[34, "persist-the-cohort-for-later"]], "Phenotype Predicates": [[42, null]], "Phenotype predicates": [[26, "phenotype-predicates"]], "Phenotype score": [[25, "phenotype-score"], [27, "phenotype-score"]], "Plot distribution of cohort variants on the protein": [[34, "plot-distribution-of-cohort-variants-on-the-protein"]], "Plot distribution of variants with respect to the protein sequence": [[23, "plot-distribution-of-variants-with-respect-to-the-protein-sequence"], [30, "plot-distribution-of-variants-with-respect-to-the-protein-sequence"]], "Postnatal growth abnormalities": [[37, "postnatal-growth-abnormalities"]], "Power": [[30, "power"]], "Predicates": [[41, null]], "Predicates for all cohort phenotypes": [[40, "predicates-for-all-cohort-phenotypes"]], "Prenatal-onset growth retardation": [[37, "prenatal-onset-growth-retardation"]], "Prepare cohort": [[23, "prepare-cohort"]], "Prepare genotype and phenotype predicates": [[23, "prepare-genotype-and-phenotype-predicates"]], "Provide the transcript coordinates manually": [[34, "provide-the-transcript-coordinates-manually"]], "Quality control": [[34, "quality-control"]], "Raw data": [[28, "raw-data"]], "Run tests": [[22, "run-tests"]], "Show cohort summary": [[23, "show-cohort-summary"]], "Showcase transcript data": [[34, "showcase-transcript-data"]], "Specify terms strategy": [[35, "specify-terms-strategy"]], "Stable release": [[22, "stable-release"]], "Standardize genotype and phenotype data": [[34, "standardize-genotype-and-phenotype-data"]], "Statistical analyses": [[24, null]], "Statistical analysis": [[26, "statistical-analysis"]], "Statistical test": [[25, "statistical-test"], [27, "statistical-test"], [28, "statistical-test"]], "Submodules": [[0, "submodules"]], "Subpackages": [[0, "subpackages"], [1, "subpackages"], [3, "subpackages"], [5, "subpackages"], [8, "subpackages"], [10, "subpackages"], [15, "subpackages"]], "Summarize all variant alleles": [[23, "summarize-all-variant-alleles"]], "Supports shape": [[4, "supports-shape"]], "Survival analysis": [[28, null]], "Survival endpoint": [[28, "survival-endpoint"]], "TBX5 frameshift vs missense": [[23, "id5"]], "TBX5 frameshift vs rest": [[26, "id1"]], "Test all terms": [[35, "test-all-terms"]], "The analysis": [[23, "the-analysis"]], "The sections of the score": [[37, "the-sections-of-the-score"]], "True path rule": [[32, "true-path-rule"]], "Tutorial": [[23, null], [29, "tutorial"]], "Types of statistical test": [[30, "types-of-statistical-test"]], "User guide": [[33, null]], "Using the De Vries scorer in code": [[37, "using-the-de-vries-scorer-in-code"]], "Variant Predicates": [[45, null]], "gpsea package": [[0, null]], "gpsea.analysis package": [[1, null]], "gpsea.analysis.mtc_filter package": [[2, null]], "gpsea.analysis.pcats package": [[3, null]], "gpsea.analysis.pcats.stats package": [[4, null]], "gpsea.analysis.predicate package": [[5, null]], "gpsea.analysis.predicate.genotype package": [[6, null]], "gpsea.analysis.predicate.phenotype package": [[7, null]], "gpsea.analysis.pscore package": [[8, null]], "gpsea.analysis.pscore.stats package": [[9, null]], "gpsea.analysis.temporal package": [[10, null]], "gpsea.analysis.temporal.endpoint package": [[11, null]], "gpsea.analysis.temporal.stats package": [[12, null]], "gpsea.config module": [[13, null]], "gpsea.io module": [[14, null]], "gpsea.model package": [[15, null]], "gpsea.model.genome package": [[16, null]], "gpsea.preprocessing package": [[17, null]], "gpsea.util module": [[18, null]], "gpsea.view package": [[19, null]], "missing_implies_phenotype_excluded": [[40, "missing-implies-phenotype-excluded"]]}, "docnames": ["apidocs/gpsea", "apidocs/gpsea.analysis", "apidocs/gpsea.analysis.mtc_filter", "apidocs/gpsea.analysis.pcats", "apidocs/gpsea.analysis.pcats.stats", "apidocs/gpsea.analysis.predicate", "apidocs/gpsea.analysis.predicate.genotype", "apidocs/gpsea.analysis.predicate.phenotype", "apidocs/gpsea.analysis.pscore", "apidocs/gpsea.analysis.pscore.stats", "apidocs/gpsea.analysis.temporal", "apidocs/gpsea.analysis.temporal.endpoint", "apidocs/gpsea.analysis.temporal.stats", "apidocs/gpsea.config", "apidocs/gpsea.io", "apidocs/gpsea.model", "apidocs/gpsea.model.genome", "apidocs/gpsea.preprocessing", "apidocs/gpsea.util", "apidocs/gpsea.view", "apidocs/modules", "index", "installation", "tutorial", "user-guide/analyses/index", "user-guide/analyses/measurements", "user-guide/analyses/phenotype-groups", "user-guide/analyses/phenotype-scores", "user-guide/analyses/survival", "user-guide/autosomal_recessive", "user-guide/exploratory", "user-guide/general_hpo_terms", "user-guide/glossary", "user-guide/index", "user-guide/input-data", "user-guide/mtc", "user-guide/predicates/allele_count", "user-guide/predicates/devries", "user-guide/predicates/diagnosis", "user-guide/predicates/genotype_predicates", "user-guide/predicates/hpo_predicate", "user-guide/predicates/index", "user-guide/predicates/phenotype_predicates", "user-guide/predicates/sex", "user-guide/predicates/variant_category", "user-guide/predicates/variant_predicates"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["apidocs/gpsea.rst", "apidocs/gpsea.analysis.rst", "apidocs/gpsea.analysis.mtc_filter.rst", "apidocs/gpsea.analysis.pcats.rst", "apidocs/gpsea.analysis.pcats.stats.rst", "apidocs/gpsea.analysis.predicate.rst", "apidocs/gpsea.analysis.predicate.genotype.rst", "apidocs/gpsea.analysis.predicate.phenotype.rst", "apidocs/gpsea.analysis.pscore.rst", "apidocs/gpsea.analysis.pscore.stats.rst", "apidocs/gpsea.analysis.temporal.rst", "apidocs/gpsea.analysis.temporal.endpoint.rst", "apidocs/gpsea.analysis.temporal.stats.rst", "apidocs/gpsea.config.rst", "apidocs/gpsea.io.rst", "apidocs/gpsea.model.rst", "apidocs/gpsea.model.genome.rst", "apidocs/gpsea.preprocessing.rst", "apidocs/gpsea.util.rst", "apidocs/gpsea.view.rst", "apidocs/modules.rst", "index.rst", "installation.rst", "tutorial.rst", "user-guide/analyses/index.rst", "user-guide/analyses/measurements.rst", "user-guide/analyses/phenotype-groups.rst", "user-guide/analyses/phenotype-scores.rst", "user-guide/analyses/survival.rst", "user-guide/autosomal_recessive.rst", "user-guide/exploratory.rst", "user-guide/general_hpo_terms.rst", "user-guide/glossary.rst", "user-guide/index.rst", "user-guide/input-data.rst", "user-guide/mtc.rst", "user-guide/predicates/allele_count.rst", "user-guide/predicates/devries.rst", "user-guide/predicates/diagnosis.rst", "user-guide/predicates/genotype_predicates.rst", "user-guide/predicates/hpo_predicate.rst", "user-guide/predicates/index.rst", "user-guide/predicates/phenotype_predicates.rst", "user-guide/predicates/sex.rst", "user-guide/predicates/variant_category.rst", "user-guide/predicates/variant_predicates.rst"], "indexentries": {"age (class in gpsea.model)": [[15, "gpsea.model.Age", false]], "age (gpsea.model.patient property)": [[15, "gpsea.model.Patient.age", false]], "age_of_death (gpsea.model.vitalstatus attribute)": [[15, "gpsea.model.VitalStatus.age_of_death", false]], "alive (gpsea.model.status attribute)": [[15, "gpsea.model.Status.ALIVE", false]], "all() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.all", false]], "all_counts (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.all_counts", false]], "all_counts (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.all_counts", false]], "all_diseases() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_diseases", false]], "all_measurements() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_measurements", false]], "all_patients (gpsea.model.cohort property)": [[15, "gpsea.model.Cohort.all_patients", false]], "all_phenotypes() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_phenotypes", false]], "all_transcript_ids (gpsea.model.cohort property)": [[15, "gpsea.model.Cohort.all_transcript_ids", false]], "all_variant_infos() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_variant_infos", false]], "all_variants() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.all_variants", false]], "allele_count() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.allele_count", false]], "allelecounter (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.AlleleCounter", false]], "alt (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.alt", false]], "analysisresult (class in gpsea.analysis)": [[1, "gpsea.analysis.AnalysisResult", false]], "annotate() (gpsea.preprocessing.defaultimprecisesvfunctionalannotator method)": [[17, "gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.functionalannotator method)": [[17, "gpsea.preprocessing.FunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.imprecisesvfunctionalannotator method)": [[17, "gpsea.preprocessing.ImpreciseSvFunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.protcachingmetadataservice method)": [[17, "gpsea.preprocessing.ProtCachingMetadataService.annotate", false]], "annotate() (gpsea.preprocessing.proteinmetadataservice method)": [[17, "gpsea.preprocessing.ProteinMetadataService.annotate", false]], "annotate() (gpsea.preprocessing.uniprotproteinmetadataservice method)": [[17, "gpsea.preprocessing.UniprotProteinMetadataService.annotate", false]], "annotate() (gpsea.preprocessing.varcachingfunctionalannotator method)": [[17, "gpsea.preprocessing.VarCachingFunctionalAnnotator.annotate", false]], "annotate() (gpsea.preprocessing.vepfunctionalannotator method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.annotate", false]], "any() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.any", false]], "apply_predicates_on_patients() (in module gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.apply_predicates_on_patients", false]], "biallelic_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.biallelic_predicate", false]], "birth() (gpsea.model.age static method)": [[15, "gpsea.model.Age.birth", false]], "cache_env (in module gpsea.config)": [[13, "gpsea.config.CACHE_ENV", false]], "cds_end (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.cds_end", false]], "cds_start (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.cds_start", false]], "change_length (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.change_length", false]], "change_length() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.change_length", false]], "chrom (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.chrom", false]], "code (gpsea.analysis.mtc_filter.phenotypemtcissue attribute)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcIssue.code", false]], "code (gpsea.model.genotype property)": [[15, "gpsea.model.Genotype.code", false]], "coding_sequence_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.CODING_SEQUENCE_VARIANT", false]], "cohort (class in gpsea.model)": [[15, "gpsea.model.Cohort", false]], "cohortcreator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.CohortCreator", false]], "cohortvariantviewer (class in gpsea.view)": [[19, "gpsea.view.CohortVariantViewer", false]], "cohortviewer (class in gpsea.view)": [[19, "gpsea.view.CohortViewer", false]], "coiled_coil (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.COILED_COIL", false]], "compare_genotype_vs_phenotype_score() (gpsea.analysis.pscore.phenotypescoreanalysis method)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysis.compare_genotype_vs_phenotype_score", false]], "compare_genotype_vs_phenotypes() (gpsea.analysis.pcats.multiphenotypeanalysis method)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysis.compare_genotype_vs_phenotypes", false]], "compare_genotype_vs_survival() (gpsea.analysis.temporal.survivalanalysis method)": [[10, "gpsea.analysis.temporal.SurvivalAnalysis.compare_genotype_vs_survival", false]], "complete_records() (gpsea.analysis.monophenotypeanalysisresult method)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.complete_records", false]], "compositional_bias (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.COMPOSITIONAL_BIAS", false]], "compute_pval() (gpsea.analysis.pcats.stats.countstatistic method)": [[4, "gpsea.analysis.pcats.stats.CountStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.pcats.stats.fisherexacttest method)": [[4, "gpsea.analysis.pcats.stats.FisherExactTest.compute_pval", false]], "compute_pval() (gpsea.analysis.pscore.stats.mannwhitneystatistic method)": [[9, "gpsea.analysis.pscore.stats.MannWhitneyStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.pscore.stats.phenotypescorestatistic method)": [[9, "gpsea.analysis.pscore.stats.PhenotypeScoreStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.pscore.stats.tteststatistic method)": [[9, "gpsea.analysis.pscore.stats.TTestStatistic.compute_pval", false]], "compute_pval() (gpsea.analysis.temporal.stats.logranktest method)": [[12, "gpsea.analysis.temporal.stats.LogRankTest.compute_pval", false]], "compute_pval() (gpsea.analysis.temporal.stats.survivalstatistic method)": [[12, "gpsea.analysis.temporal.stats.SurvivalStatistic.compute_pval", false]], "compute_survival() (gpsea.analysis.temporal.endpoint method)": [[10, "gpsea.analysis.temporal.Endpoint.compute_survival", false]], "configure_caching_cohort_creator() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_caching_cohort_creator", false]], "configure_cohort_creator() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_cohort_creator", false]], "configure_default_protein_metadata_service() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_default_protein_metadata_service", false]], "configure_hpo_term_analysis() (in module gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.configure_hpo_term_analysis", false]], "configure_protein_metadata_service() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.configure_protein_metadata_service", false]], "contains() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.contains", false]], "contains() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.contains", false]], "contains_pos() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.contains_pos", false]], "contig (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Contig", false]], "contig (gpsea.model.genome.genomicregion property)": [[16, "gpsea.model.genome.GenomicRegion.contig", false]], "contig_by_name() (gpsea.model.genome.genomebuild method)": [[16, "gpsea.model.genome.GenomeBuild.contig_by_name", false]], "contigs (gpsea.model.genome.genomebuild property)": [[16, "gpsea.model.genome.GenomeBuild.contigs", false]], "corrected_pvals (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.corrected_pvals", false]], "corrected_pvals (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.corrected_pvals", false]], "count() (gpsea.analysis.predicate.genotype.allelecounter method)": [[6, "gpsea.analysis.predicate.genotype.AlleleCounter.count", false]], "count_alive() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_alive", false]], "count_deceased() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_deceased", false]], "count_distinct_diseases() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_distinct_diseases", false]], "count_distinct_hpo_terms() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_distinct_hpo_terms", false]], "count_distinct_measurements() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_distinct_measurements", false]], "count_females() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_females", false]], "count_males() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_males", false]], "count_unique_diseases() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.count_unique_diseases", false]], "count_unique_measurements() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.count_unique_measurements", false]], "count_unique_phenotypes() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.count_unique_phenotypes", false]], "count_unknown_sex() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_unknown_sex", false]], "count_unknown_vital_status() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_unknown_vital_status", false]], "count_with_age_of_last_encounter() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_with_age_of_last_encounter", false]], "count_with_disease_onset() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.count_with_disease_onset", false]], "countingphenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer", false]], "countstatistic (class in gpsea.analysis.pcats.stats)": [[4, "gpsea.analysis.pcats.stats.CountStatistic", false]], "create() (gpsea.model.proteinfeature static method)": [[15, "gpsea.model.ProteinFeature.create", false]], "create_variant_from_scratch() (gpsea.model.variant static method)": [[15, "gpsea.model.Variant.create_variant_from_scratch", false]], "curie (gpsea.model.varianteffect property)": [[15, "gpsea.model.VariantEffect.curie", false]], "data (gpsea.analysis.monophenotypeanalysisresult property)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.data", false]], "data_columns (gpsea.analysis.monophenotypeanalysisresult attribute)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.DATA_COLUMNS", false]], "days (gpsea.model.age property)": [[15, "gpsea.model.Age.days", false]], "days_in_month (gpsea.model.age attribute)": [[15, "gpsea.model.Age.DAYS_IN_MONTH", false]], "days_in_week (gpsea.model.age attribute)": [[15, "gpsea.model.Age.DAYS_IN_WEEK", false]], "days_in_year (gpsea.model.age attribute)": [[15, "gpsea.model.Age.DAYS_IN_YEAR", false]], "death() (in module gpsea.analysis.temporal.endpoint)": [[11, "gpsea.analysis.temporal.endpoint.death", false]], "deceased (gpsea.model.status attribute)": [[15, "gpsea.model.Status.DECEASED", false]], "default() (gpsea.io.gpseajsonencoder method)": [[14, "gpsea.io.GpseaJSONEncoder.default", false]], "default_cache_path (in module gpsea.config)": [[13, "gpsea.config.DEFAULT_CACHE_PATH", false]], "default_filter() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter", false]], "default_parser() (gpsea.preprocessing.phenopacketontologytermonsetparser static method)": [[17, "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser.default_parser", false]], "defaultimprecisesvfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator", false]], "del (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.DEL", false]], "description (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.description", false]], "description (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.description", false]], "description (gpsea.analysis.pscore.countingphenotypescorer property)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.description", false]], "description (gpsea.analysis.pscore.devriesphenotypescorer property)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.description", false]], "description (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.description", false]], "devriesphenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer", false]], "diagnosis_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.diagnosis_predicate", false]], "disease (class in gpsea.model)": [[15, "gpsea.model.Disease", false]], "disease_by_id() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.disease_by_id", false]], "disease_onset() (in module gpsea.analysis.temporal.endpoint)": [[11, "gpsea.analysis.temporal.endpoint.disease_onset", false]], "diseaseanalysis (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.DiseaseAnalysis", false]], "diseasepresencepredicate (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate", false]], "diseases (gpsea.model.patient property)": [[15, "gpsea.model.Patient.diseases", false]], "diseaseviewer (class in gpsea.view)": [[19, "gpsea.view.DiseaseViewer", false]], "distance_to() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.distance_to", false]], "distance_to() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.distance_to", false]], "domain (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.DOMAIN", false]], "domains() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.domains", false]], "downstream_gene_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.DOWNSTREAM_GENE_VARIANT", false]], "draw_fig() (gpsea.view.proteinvisualizer method)": [[19, "gpsea.view.ProteinVisualizer.draw_fig", false]], "draw_protein_diagram() (gpsea.view.proteinvisualizer method)": [[19, "gpsea.view.ProteinVisualizer.draw_protein_diagram", false]], "draw_variants() (gpsea.view.varianttranscriptvisualizer method)": [[19, "gpsea.view.VariantTranscriptVisualizer.draw_variants", false]], "dup (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.DUP", false]], "empty() (gpsea.model.genotypes static method)": [[15, "gpsea.model.Genotypes.empty", false]], "end (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.end", false]], "end (gpsea.model.genome.region property)": [[16, "gpsea.model.genome.Region.end", false]], "end (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.end", false]], "end_on_strand() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.end_on_strand", false]], "endpoint (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.Endpoint", false]], "endpoint (gpsea.analysis.temporal.survivalanalysisresult property)": [[10, "gpsea.analysis.temporal.SurvivalAnalysisResult.endpoint", false]], "excluded_diseases() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.excluded_diseases", false]], "excluded_phenotypes() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.excluded_phenotypes", false]], "exon() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.exon", false]], "exons (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.exons", false]], "fail() (gpsea.analysis.mtc_filter.phenotypemtcresult static method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.fail", false]], "feature_elongation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FEATURE_ELONGATION", false]], "feature_truncation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FEATURE_TRUNCATION", false]], "feature_type (gpsea.model.proteinfeature property)": [[15, "gpsea.model.ProteinFeature.feature_type", false]], "featureinfo (class in gpsea.model)": [[15, "gpsea.model.FeatureInfo", false]], "featuretype (class in gpsea.model)": [[15, "gpsea.model.FeatureType", false]], "female (gpsea.model.sex attribute)": [[15, "gpsea.model.Sex.FEMALE", false]], "fetch() (gpsea.preprocessing.transcriptcoordinateservice method)": [[17, "gpsea.preprocessing.TranscriptCoordinateService.fetch", false]], "fetch() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.fetch", false]], "fetch_for_gene() (gpsea.preprocessing.genecoordinateservice method)": [[17, "gpsea.preprocessing.GeneCoordinateService.fetch_for_gene", false]], "fetch_for_gene() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.fetch_for_gene", false]], "fetch_response() (gpsea.preprocessing.vepfunctionalannotator method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.fetch_response", false]], "filter() (gpsea.analysis.mtc_filter.hpomtcfilter method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.filter", false]], "filter() (gpsea.analysis.mtc_filter.phenotypemtcfilter method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter", false]], "filter() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter", false]], "filter() (gpsea.analysis.mtc_filter.usealltermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter", false]], "filter_method_name() (gpsea.analysis.mtc_filter.hpomtcfilter method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.filter_method_name", false]], "filter_method_name() (gpsea.analysis.mtc_filter.phenotypemtcfilter method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.filter_method_name", false]], "filter_method_name() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.filter_method_name", false]], "filter_method_name() (gpsea.analysis.mtc_filter.usealltermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.filter_method_name", false]], "find_coordinates() (gpsea.preprocessing.phenopacketvariantcoordinatefinder method)": [[17, "gpsea.preprocessing.PhenopacketVariantCoordinateFinder.find_coordinates", false]], "find_coordinates() (gpsea.preprocessing.variantcoordinatefinder method)": [[17, "gpsea.preprocessing.VariantCoordinateFinder.find_coordinates", false]], "find_coordinates() (gpsea.preprocessing.vvhgvsvariantcoordinatefinder method)": [[17, "gpsea.preprocessing.VVHgvsVariantCoordinateFinder.find_coordinates", false]], "fisherexacttest (class in gpsea.analysis.pcats.stats)": [[4, "gpsea.analysis.pcats.stats.FisherExactTest", false]], "five_prime_utr_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FIVE_PRIME_UTR_VARIANT", false]], "for_sample() (gpsea.model.genotypes method)": [[15, "gpsea.model.Genotypes.for_sample", false]], "format_as_string() (gpsea.view.formatter method)": [[19, "gpsea.view.Formatter.format_as_string", false]], "format_as_string() (gpsea.view.variantformatter method)": [[19, "gpsea.view.VariantFormatter.format_as_string", false]], "format_coordinates_for_vep_query() (gpsea.preprocessing.vepfunctionalannotator static method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.format_coordinates_for_vep_query", false]], "formatter (class in gpsea.view)": [[19, "gpsea.view.Formatter", false]], "frameshift_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.FRAMESHIFT_VARIANT", false]], "from_feature_frame() (gpsea.model.proteinmetadata static method)": [[15, "gpsea.model.ProteinMetadata.from_feature_frame", false]], "from_iso8601_period() (gpsea.model.age static method)": [[15, "gpsea.model.Age.from_iso8601_period", false]], "from_mapping() (gpsea.model.genotypes static method)": [[15, "gpsea.model.Genotypes.from_mapping", false]], "from_measurement_id() (gpsea.analysis.pscore.measurementphenotypescorer static method)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.from_measurement_id", false]], "from_patients() (gpsea.model.cohort static method)": [[15, "gpsea.model.Cohort.from_patients", false]], "from_query_curies() (gpsea.analysis.pscore.countingphenotypescorer static method)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.from_query_curies", false]], "from_raw_parts() (gpsea.model.disease static method)": [[15, "gpsea.model.Disease.from_raw_parts", false]], "from_raw_parts() (gpsea.model.patient static method)": [[15, "gpsea.model.Patient.from_raw_parts", false]], "from_raw_parts() (gpsea.model.phenotype static method)": [[15, "gpsea.model.Phenotype.from_raw_parts", false]], "from_string() (gpsea.model.featuretype static method)": [[15, "gpsea.model.FeatureType.from_string", false]], "from_term() (gpsea.model.phenotype static method)": [[15, "gpsea.model.Phenotype.from_term", false]], "from_uniprot_json() (gpsea.model.proteinmetadata static method)": [[15, "gpsea.model.ProteinMetadata.from_uniprot_json", false]], "from_vcf_literal() (gpsea.model.variantcoordinates static method)": [[15, "gpsea.model.VariantCoordinates.from_vcf_literal", false]], "from_vcf_symbolic() (gpsea.model.variantcoordinates static method)": [[15, "gpsea.model.VariantCoordinates.from_vcf_symbolic", false]], "functionalannotationaware (class in gpsea.model)": [[15, "gpsea.model.FunctionalAnnotationAware", false]], "functionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.FunctionalAnnotator", false]], "genbank_acc (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.genbank_acc", false]], "gene() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.gene", false]], "gene_id (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.gene_id", false]], "gene_id (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.gene_id", false]], "gene_id (gpsea.model.transcriptinfoaware property)": [[15, "gpsea.model.TranscriptInfoAware.gene_id", false]], "gene_symbol (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.gene_symbol", false]], "genecoordinateservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.GeneCoordinateService", false]], "genome_build_id (gpsea.model.genome.genomebuild property)": [[16, "gpsea.model.genome.GenomeBuild.genome_build_id", false]], "genomebuild (class in gpsea.model.genome)": [[16, "gpsea.model.genome.GenomeBuild", false]], "genomebuildidentifier (class in gpsea.model.genome)": [[16, "gpsea.model.genome.GenomeBuildIdentifier", false]], "genomicregion (class in gpsea.model.genome)": [[16, "gpsea.model.genome.GenomicRegion", false]], "genotype (class in gpsea.model)": [[15, "gpsea.model.Genotype", false]], "genotype_for_sample() (gpsea.model.genotyped method)": [[15, "gpsea.model.Genotyped.genotype_for_sample", false]], "genotyped (class in gpsea.model)": [[15, "gpsea.model.Genotyped", false]], "genotypepolypredicate (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.GenotypePolyPredicate", false]], "genotypes (class in gpsea.model)": [[15, "gpsea.model.Genotypes", false]], "genotypes (gpsea.model.genotyped property)": [[15, "gpsea.model.Genotyped.genotypes", false]], "genotypes (gpsea.model.variant property)": [[15, "gpsea.model.Variant.genotypes", false]], "gestational (gpsea.model.timeline attribute)": [[15, "gpsea.model.Timeline.GESTATIONAL", false]], "gestational() (gpsea.model.age static method)": [[15, "gpsea.model.Age.gestational", false]], "gestational_days() (gpsea.model.age static method)": [[15, "gpsea.model.Age.gestational_days", false]], "get_annotations() (gpsea.preprocessing.proteinannotationcache method)": [[17, "gpsea.preprocessing.ProteinAnnotationCache.get_annotations", false]], "get_annotations() (gpsea.preprocessing.variantannotationcache method)": [[17, "gpsea.preprocessing.VariantAnnotationCache.get_annotations", false]], "get_cache_dir_path() (in module gpsea.config)": [[13, "gpsea.config.get_cache_dir_path", false]], "get_categories() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_categories", false]], "get_categorizations() (gpsea.analysis.predicate.phenotype.diseasepresencepredicate method)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.get_categorizations", false]], "get_categorizations() (gpsea.analysis.predicate.phenotype.hpopredicate method)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.get_categorizations", false]], "get_categorizations() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_categorizations", false]], "get_category() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_category", false]], "get_category_name() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.get_category_name", false]], "get_cds_regions() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_cds_regions", false]], "get_coding_base_count() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_coding_base_count", false]], "get_codon_count() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_codon_count", false]], "get_excluded_count() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.get_excluded_count", false]], "get_features_variant_overlaps() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.get_features_variant_overlaps", false]], "get_five_prime_utrs() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_five_prime_utrs", false]], "get_hgvs_cdna_by_tx_id() (gpsea.model.functionalannotationaware method)": [[15, "gpsea.model.FunctionalAnnotationAware.get_hgvs_cdna_by_tx_id", false]], "get_maximum_group_observed_hpo_frequency() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.get_maximum_group_observed_HPO_frequency", false]], "get_number_of_observed_hpo_observations() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.get_number_of_observed_hpo_observations", false]], "get_patient_ids() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.get_patient_ids", false]], "get_preferred_tx_annotation() (gpsea.model.functionalannotationaware method)": [[15, "gpsea.model.FunctionalAnnotationAware.get_preferred_tx_annotation", false]], "get_question() (gpsea.analysis.predicate.genotype.allelecounter method)": [[6, "gpsea.analysis.predicate.genotype.AlleleCounter.get_question", false]], "get_question() (gpsea.analysis.predicate.genotype.variantpredicate method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicate.get_question", false]], "get_response() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.get_response", false]], "get_three_prime_utrs() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.get_three_prime_utrs", false]], "get_tx_anno_by_tx_id() (gpsea.model.functionalannotationaware method)": [[15, "gpsea.model.FunctionalAnnotationAware.get_tx_anno_by_tx_id", false]], "get_variant_by_key() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.get_variant_by_key", false]], "gpsea": [[0, "module-gpsea", false]], "gpsea.analysis": [[1, "module-gpsea.analysis", false]], "gpsea.analysis.mtc_filter": [[2, "module-gpsea.analysis.mtc_filter", false]], "gpsea.analysis.pcats": [[3, "module-gpsea.analysis.pcats", false]], "gpsea.analysis.pcats.stats": [[4, "module-gpsea.analysis.pcats.stats", false]], "gpsea.analysis.predicate": [[5, "module-gpsea.analysis.predicate", false]], "gpsea.analysis.predicate.genotype": [[6, "module-gpsea.analysis.predicate.genotype", false]], "gpsea.analysis.predicate.phenotype": [[7, "module-gpsea.analysis.predicate.phenotype", false]], "gpsea.analysis.pscore": [[8, "module-gpsea.analysis.pscore", false]], "gpsea.analysis.pscore.stats": [[9, "module-gpsea.analysis.pscore.stats", false]], "gpsea.analysis.temporal": [[10, "module-gpsea.analysis.temporal", false]], "gpsea.analysis.temporal.endpoint": [[11, "module-gpsea.analysis.temporal.endpoint", false]], "gpsea.analysis.temporal.stats": [[12, "module-gpsea.analysis.temporal.stats", false]], "gpsea.config": [[13, "module-gpsea.config", false]], "gpsea.io": [[14, "module-gpsea.io", false]], "gpsea.model": [[15, "module-gpsea.model", false]], "gpsea.model.genome": [[16, "module-gpsea.model.genome", false]], "gpsea.preprocessing": [[17, "module-gpsea.preprocessing", false]], "gpsea.util": [[18, "module-gpsea.util", false]], "gpsea.view": [[19, "module-gpsea.view", false]], "gpseajsondecoder (class in gpsea.io)": [[14, "gpsea.io.GpseaJSONDecoder", false]], "gpseajsonencoder (class in gpsea.io)": [[14, "gpsea.io.GpseaJSONEncoder", false]], "gpseareport (class in gpsea.view)": [[19, "gpsea.view.GpseaReport", false]], "group_labels (gpsea.analysis.predicate.polypredicate property)": [[5, "gpsea.analysis.predicate.PolyPredicate.group_labels", false]], "gt_col (gpsea.analysis.monophenotypeanalysisresult attribute)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.GT_COL", false]], "gt_predicate (gpsea.analysis.analysisresult property)": [[1, "gpsea.analysis.AnalysisResult.gt_predicate", false]], "has_sv_info() (gpsea.model.variantinfo method)": [[15, "gpsea.model.VariantInfo.has_sv_info", false]], "has_variant_coordinates() (gpsea.model.variantinfo method)": [[15, "gpsea.model.VariantInfo.has_variant_coordinates", false]], "hemizygous (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HEMIZYGOUS", false]], "heterozygous (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HETEROZYGOUS", false]], "hgvs_cdna (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.hgvs_cdna", false]], "hgvsp (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.hgvsp", false]], "homozygous_alternate (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HOMOZYGOUS_ALTERNATE", false]], "homozygous_reference (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.HOMOZYGOUS_REFERENCE", false]], "hpo_onset() (in module gpsea.analysis.temporal.endpoint)": [[11, "gpsea.analysis.temporal.endpoint.hpo_onset", false]], "hpomtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter", false]], "hpopredicate (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate", false]], "hpotermanalysis (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.HpoTermAnalysis", false]], "hpotermanalysisresult (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult", false]], "identifier (gpsea.model.disease property)": [[15, "gpsea.model.Disease.identifier", false]], "identifier (gpsea.model.genome.genomebuild property)": [[16, "gpsea.model.genome.GenomeBuild.identifier", false]], "identifier (gpsea.model.genome.genomebuildidentifier property)": [[16, "gpsea.model.genome.GenomeBuildIdentifier.identifier", false]], "identifier (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.identifier", false]], "identifier (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.identifier", false]], "identifier (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.identifier", false]], "imprecisesvfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ImpreciseSvFunctionalAnnotator", false]], "imprecisesvinfo (class in gpsea.model)": [[15, "gpsea.model.ImpreciseSvInfo", false]], "incomplete_terminal_codon_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INCOMPLETE_TERMINAL_CODON_VARIANT", false]], "info (gpsea.model.proteinfeature property)": [[15, "gpsea.model.ProteinFeature.info", false]], "inframe_deletion (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INFRAME_DELETION", false]], "inframe_insertion (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INFRAME_INSERTION", false]], "ins (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.INS", false]], "intergenic_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INTERGENIC_VARIANT", false]], "intron_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.INTRON_VARIANT", false]], "inv (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.INV", false]], "is_alive (gpsea.model.vitalstatus property)": [[15, "gpsea.model.VitalStatus.is_alive", false]], "is_censored (gpsea.analysis.temporal.survival attribute)": [[10, "gpsea.analysis.temporal.Survival.is_censored", false]], "is_coding() (gpsea.model.transcriptcoordinates method)": [[15, "gpsea.model.TranscriptCoordinates.is_coding", false]], "is_deceased (gpsea.model.vitalstatus property)": [[15, "gpsea.model.VitalStatus.is_deceased", false]], "is_empty() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.is_empty", false]], "is_female() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_female", false]], "is_filtered_out() (gpsea.analysis.mtc_filter.phenotypemtcresult method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_filtered_out", false]], "is_gestational (gpsea.model.age property)": [[15, "gpsea.model.Age.is_gestational", false]], "is_large_imprecise_sv() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.is_large_imprecise_sv", false]], "is_male() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_male", false]], "is_negative() (gpsea.model.genome.strand method)": [[16, "gpsea.model.genome.Strand.is_negative", false]], "is_observed (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.is_observed", false]], "is_ok() (gpsea.preprocessing.preprocessingvalidationresult method)": [[17, "gpsea.preprocessing.PreprocessingValidationResult.is_ok", false]], "is_passed() (gpsea.analysis.mtc_filter.phenotypemtcresult method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.is_passed", false]], "is_positive() (gpsea.model.genome.strand method)": [[16, "gpsea.model.genome.Strand.is_positive", false]], "is_postnatal (gpsea.model.age property)": [[15, "gpsea.model.Age.is_postnatal", false]], "is_preferred (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.is_preferred", false]], "is_preferred (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.is_preferred", false]], "is_present (gpsea.model.disease property)": [[15, "gpsea.model.Disease.is_present", false]], "is_present (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.is_present", false]], "is_provided() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_provided", false]], "is_structural() (gpsea.model.variantcoordinates method)": [[15, "gpsea.model.VariantCoordinates.is_structural", false]], "is_structural() (gpsea.model.variantinfo method)": [[15, "gpsea.model.VariantInfo.is_structural", false]], "is_structural_deletion() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.is_structural_deletion", false]], "is_structural_variant() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.is_structural_variant", false]], "is_unknown (gpsea.model.vitalstatus property)": [[15, "gpsea.model.VitalStatus.is_unknown", false]], "is_unknown() (gpsea.model.sex method)": [[15, "gpsea.model.Sex.is_unknown", false]], "iso8601pt (gpsea.model.age attribute)": [[15, "gpsea.model.Age.ISO8601PT", false]], "label (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.label", false]], "label (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.label", false]], "label (gpsea.model.samplelabels property)": [[15, "gpsea.model.SampleLabels.label", false]], "label_summary() (gpsea.model.samplelabels method)": [[15, "gpsea.model.SampleLabels.label_summary", false]], "labels (gpsea.model.patient property)": [[15, "gpsea.model.Patient.labels", false]], "last_menstrual_period() (gpsea.model.age static method)": [[15, "gpsea.model.Age.last_menstrual_period", false]], "list_all_diseases() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_all_diseases", false]], "list_all_proteins() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_all_proteins", false]], "list_all_variants() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_all_variants", false]], "list_measurements() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_measurements", false]], "list_present_phenotypes() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.list_present_phenotypes", false]], "load_phenopacket_files() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.load_phenopacket_files", false]], "load_phenopacket_folder() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.load_phenopacket_folder", false]], "load_phenopackets() (in module gpsea.preprocessing)": [[17, "gpsea.preprocessing.load_phenopackets", false]], "logranktest (class in gpsea.analysis.temporal.stats)": [[12, "gpsea.analysis.temporal.stats.LogRankTest", false]], "major_assembly (gpsea.model.genome.genomebuildidentifier property)": [[16, "gpsea.model.genome.GenomeBuildIdentifier.major_assembly", false]], "male (gpsea.model.sex attribute)": [[15, "gpsea.model.Sex.MALE", false]], "mannwhitneystatistic (class in gpsea.analysis.pscore.stats)": [[9, "gpsea.analysis.pscore.stats.MannWhitneyStatistic", false]], "marker_counts (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.marker_counts", false]], "mature_mirna_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.MATURE_MIRNA_VARIANT", false]], "measurement (class in gpsea.model)": [[15, "gpsea.model.Measurement", false]], "measurement_by_id() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.measurement_by_id", false]], "measurementphenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer", false]], "measurements (gpsea.model.patient property)": [[15, "gpsea.model.Patient.measurements", false]], "meta_label (gpsea.model.samplelabels property)": [[15, "gpsea.model.SampleLabels.meta_label", false]], "missense_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.MISSENSE_VARIANT", false]], "mnv (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.MNV", false]], "module": [[0, "module-gpsea", false], [1, "module-gpsea.analysis", false], [2, "module-gpsea.analysis.mtc_filter", false], [3, "module-gpsea.analysis.pcats", false], [4, "module-gpsea.analysis.pcats.stats", false], [5, "module-gpsea.analysis.predicate", false], [6, "module-gpsea.analysis.predicate.genotype", false], [7, "module-gpsea.analysis.predicate.phenotype", false], [8, "module-gpsea.analysis.pscore", false], [9, "module-gpsea.analysis.pscore.stats", false], [10, "module-gpsea.analysis.temporal", false], [11, "module-gpsea.analysis.temporal.endpoint", false], [12, "module-gpsea.analysis.temporal.stats", false], [13, "module-gpsea.config", false], [14, "module-gpsea.io", false], [15, "module-gpsea.model", false], [16, "module-gpsea.model.genome", false], [17, "module-gpsea.preprocessing", false], [18, "module-gpsea.util", false], [19, "module-gpsea.view", false]], "monoallelic_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.monoallelic_predicate", false]], "monophenotypeanalysisresult (class in gpsea.analysis)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult", false]], "motif (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.MOTIF", false]], "motifs() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.motifs", false]], "mtc_correction (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.mtc_correction", false]], "mtc_correction (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.mtc_correction", false]], "mtc_filter_name (gpsea.analysis.pcats.hpotermanalysisresult property)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_filter_name", false]], "mtc_filter_results (gpsea.analysis.pcats.hpotermanalysisresult property)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult.mtc_filter_results", false]], "mtc_issue (gpsea.analysis.mtc_filter.phenotypemtcresult property)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.mtc_issue", false]], "mtcstatsviewer (class in gpsea.view)": [[19, "gpsea.view.MtcStatsViewer", false]], "multiphenotypeanalysis (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysis", false]], "multiphenotypeanalysisresult (class in gpsea.analysis)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult", false]], "multiphenotypeanalysisresult (class in gpsea.analysis.pcats)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult", false]], "n_categorizations() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.n_categorizations", false]], "n_filtered_out() (gpsea.analysis.pcats.hpotermanalysisresult method)": [[3, "gpsea.analysis.pcats.HpoTermAnalysisResult.n_filtered_out", false]], "n_significant_for_alpha() (gpsea.analysis.multiphenotypeanalysisresult method)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.n_significant_for_alpha", false]], "n_significant_for_alpha() (gpsea.analysis.pcats.multiphenotypeanalysisresult method)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.n_significant_for_alpha", false]], "n_usable (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.n_usable", false]], "n_usable (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.n_usable", false]], "name (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.name", false]], "name (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.name", false]], "name (gpsea.analysis.pscore.countingphenotypescorer property)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.name", false]], "name (gpsea.analysis.pscore.devriesphenotypescorer property)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.name", false]], "name (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.name", false]], "name (gpsea.analysis.statistic property)": [[1, "gpsea.analysis.Statistic.name", false]], "name (gpsea.model.disease property)": [[15, "gpsea.model.Disease.name", false]], "name (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.name", false]], "name (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.name", false]], "name (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.name", false]], "negative (gpsea.model.genome.strand attribute)": [[16, "gpsea.model.genome.Strand.NEGATIVE", false]], "nmd_transcript_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.NMD_TRANSCRIPT_VARIANT", false]], "no_call (gpsea.model.genotype attribute)": [[15, "gpsea.model.Genotype.NO_CALL", false]], "no_genotype_has_more_than_one_hpo (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO", false]], "non_coding_transcript_exon_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.NON_CODING_TRANSCRIPT_EXON_VARIANT", false]], "non_coding_transcript_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.NON_CODING_TRANSCRIPT_VARIANT", false]], "non_specified_term (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.NON_SPECIFIED_TERM", false]], "noncoding_effects (gpsea.preprocessing.vepfunctionalannotator attribute)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.NONCODING_EFFECTS", false]], "object_hook() (gpsea.io.gpseajsondecoder static method)": [[14, "gpsea.io.GpseaJSONDecoder.object_hook", false]], "observed (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.observed", false]], "ok (gpsea.analysis.mtc_filter.phenotypemtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.OK", false]], "ok() (gpsea.analysis.mtc_filter.phenotypemtcresult static method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.ok", false]], "one_genotype_has_zero_hpo_observations() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.one_genotype_has_zero_hpo_observations", false]], "onset (gpsea.model.disease property)": [[15, "gpsea.model.Disease.onset", false]], "onset (gpsea.model.phenotype property)": [[15, "gpsea.model.Phenotype.onset", false]], "open_resource() (in module gpsea.util)": [[18, "gpsea.util.open_resource", false]], "open_text_io_handle_for_reading() (in module gpsea.util)": [[18, "gpsea.util.open_text_io_handle_for_reading", false]], "open_text_io_handle_for_writing() (in module gpsea.util)": [[18, "gpsea.util.open_text_io_handle_for_writing", false]], "opposite() (gpsea.model.genome.strand method)": [[16, "gpsea.model.genome.Strand.opposite", false]], "overlapping_exons (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.overlapping_exons", false]], "overlaps_with() (gpsea.model.featureinfo method)": [[15, "gpsea.model.FeatureInfo.overlaps_with", false]], "overlaps_with() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.overlaps_with", false]], "overlaps_with() (gpsea.model.genome.region method)": [[16, "gpsea.model.genome.Region.overlaps_with", false]], "parse_multiple() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.parse_multiple", false]], "parse_response() (gpsea.preprocessing.vvmulticoordinateservice method)": [[17, "gpsea.preprocessing.VVMultiCoordinateService.parse_response", false]], "parse_uniprot_json() (gpsea.preprocessing.uniprotproteinmetadataservice static method)": [[17, "gpsea.preprocessing.UniprotProteinMetadataService.parse_uniprot_json", false]], "patch (gpsea.model.genome.genomebuildidentifier property)": [[16, "gpsea.model.genome.GenomeBuildIdentifier.patch", false]], "patient (class in gpsea.model)": [[15, "gpsea.model.Patient", false]], "patient_id (gpsea.model.patient property)": [[15, "gpsea.model.Patient.patient_id", false]], "patientcreator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PatientCreator", false]], "ph_col (gpsea.analysis.monophenotypeanalysisresult attribute)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.PH_COL", false]], "pheno_predicates (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.pheno_predicates", false]], "pheno_predicates (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.pheno_predicates", false]], "phenopacketontologytermonsetparser (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser", false]], "phenopacketpatientcreator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PhenopacketPatientCreator", false]], "phenopacketvariantcoordinatefinder (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PhenopacketVariantCoordinateFinder", false]], "phenotype (class in gpsea.model)": [[15, "gpsea.model.Phenotype", false]], "phenotype (gpsea.analysis.monophenotypeanalysisresult property)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.phenotypecategorization property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypeCategorization.phenotype", false]], "phenotype (gpsea.analysis.predicate.phenotype.phenotypepolypredicate property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.phenotype", false]], "phenotype_by_id() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.phenotype_by_id", false]], "phenotype_scorer() (gpsea.analysis.pscore.phenotypescoreanalysisresult method)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult.phenotype_scorer", false]], "phenotypecategorization (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypeCategorization", false]], "phenotypemtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter", false]], "phenotypemtcissue (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcIssue", false]], "phenotypemtcresult (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult", false]], "phenotypepolypredicate (class in gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate", false]], "phenotypes (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.phenotypes", false]], "phenotypes (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.phenotypes", false]], "phenotypes (gpsea.model.patient property)": [[15, "gpsea.model.Patient.phenotypes", false]], "phenotypescoreanalysis (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysis", false]], "phenotypescoreanalysisresult (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult", false]], "phenotypescorer (class in gpsea.analysis.pscore)": [[8, "gpsea.analysis.pscore.PhenotypeScorer", false]], "phenotypescorestatistic (class in gpsea.analysis.pscore.stats)": [[9, "gpsea.analysis.pscore.stats.PhenotypeScoreStatistic", false]], "plot_boxplots() (gpsea.analysis.pscore.phenotypescoreanalysisresult method)": [[8, "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult.plot_boxplots", false]], "plot_kaplan_meier_curves() (gpsea.analysis.temporal.survivalanalysisresult method)": [[10, "gpsea.analysis.temporal.SurvivalAnalysisResult.plot_kaplan_meier_curves", false]], "policy (gpsea.preprocessing.preprocessingvalidationresult property)": [[17, "gpsea.preprocessing.PreprocessingValidationResult.policy", false]], "polypredicate (class in gpsea.analysis.predicate)": [[5, "gpsea.analysis.predicate.PolyPredicate", false]], "positive (gpsea.model.genome.strand attribute)": [[16, "gpsea.model.genome.Strand.POSITIVE", false]], "possible_results() (gpsea.analysis.mtc_filter.hpomtcfilter method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.possible_results", false]], "possible_results() (gpsea.analysis.mtc_filter.phenotypemtcfilter method)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcFilter.possible_results", false]], "possible_results() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.possible_results", false]], "possible_results() (gpsea.analysis.mtc_filter.usealltermsmtcfilter method)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter.possible_results", false]], "postnatal (gpsea.model.timeline attribute)": [[15, "gpsea.model.Timeline.POSTNATAL", false]], "postnatal() (gpsea.model.age static method)": [[15, "gpsea.model.Age.postnatal", false]], "postnatal_days() (gpsea.model.age static method)": [[15, "gpsea.model.Age.postnatal_days", false]], "postnatal_years() (gpsea.model.age static method)": [[15, "gpsea.model.Age.postnatal_years", false]], "prepare_hpo_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.prepare_hpo_terms_of_interest", false]], "prepare_predicates_for_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)": [[7, "gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest", false]], "preprocessingvalidationresult (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.PreprocessingValidationResult", false]], "present_diseases() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.present_diseases", false]], "present_phenotype_categorization (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.present_phenotype_categorization", false]], "present_phenotype_categorization (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.present_phenotype_categorization", false]], "present_phenotype_categorization (gpsea.analysis.predicate.phenotype.phenotypepolypredicate property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.present_phenotype_categorization", false]], "present_phenotype_category (gpsea.analysis.predicate.phenotype.phenotypepolypredicate property)": [[7, "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate.present_phenotype_category", false]], "present_phenotypes() (gpsea.model.patient method)": [[15, "gpsea.model.Patient.present_phenotypes", false]], "process() (gpsea.preprocessing.cohortcreator method)": [[17, "gpsea.preprocessing.CohortCreator.process", false]], "process() (gpsea.preprocessing.patientcreator method)": [[17, "gpsea.preprocessing.PatientCreator.process", false]], "process() (gpsea.preprocessing.phenopacketontologytermonsetparser method)": [[17, "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser.process", false]], "process() (gpsea.preprocessing.phenopacketpatientcreator method)": [[17, "gpsea.preprocessing.PhenopacketPatientCreator.process", false]], "process() (gpsea.view.cohortvariantviewer method)": [[19, "gpsea.view.CohortVariantViewer.process", false]], "process() (gpsea.view.cohortviewer method)": [[19, "gpsea.view.CohortViewer.process", false]], "process() (gpsea.view.diseaseviewer method)": [[19, "gpsea.view.DiseaseViewer.process", false]], "process() (gpsea.view.mtcstatsviewer method)": [[19, "gpsea.view.MtcStatsViewer.process", false]], "process() (gpsea.view.proteinvariantviewer method)": [[19, "gpsea.view.ProteinVariantViewer.process", false]], "process_response() (gpsea.preprocessing.vepfunctionalannotator method)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator.process_response", false]], "protcachingmetadataservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ProtCachingMetadataService", false]], "protein_altering_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.PROTEIN_ALTERING_VARIANT", false]], "protein_effect_location (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.protein_effect_location", false]], "protein_feature() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.protein_feature", false]], "protein_feature_ends (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_ends", false]], "protein_feature_names (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_names", false]], "protein_feature_starts (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_starts", false]], "protein_feature_type() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.protein_feature_type", false]], "protein_feature_types (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_feature_types", false]], "protein_features (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.protein_features", false]], "protein_id (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.protein_id", false]], "protein_id (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.protein_id", false]], "protein_id (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_id", false]], "protein_length (gpsea.model.proteinmetadata property)": [[15, "gpsea.model.ProteinMetadata.protein_length", false]], "protein_length (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_length", false]], "protein_metadata (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.protein_metadata", false]], "proteinannotationcache (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ProteinAnnotationCache", false]], "proteinfeature (class in gpsea.model)": [[15, "gpsea.model.ProteinFeature", false]], "proteinmetadata (class in gpsea.model)": [[15, "gpsea.model.ProteinMetadata", false]], "proteinmetadataservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.ProteinMetadataService", false]], "proteinvariantviewer (class in gpsea.view)": [[19, "gpsea.view.ProteinVariantViewer", false]], "proteinvisualizable (class in gpsea.view)": [[19, "gpsea.view.ProteinVisualizable", false]], "proteinvisualizer (class in gpsea.view)": [[19, "gpsea.view.ProteinVisualizer", false]], "pval (gpsea.analysis.monophenotypeanalysisresult property)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.pval", false]], "pval (gpsea.analysis.statisticresult property)": [[1, "gpsea.analysis.StatisticResult.pval", false]], "pvals (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.pvals", false]], "pvals (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.pvals", false]], "reason (gpsea.analysis.mtc_filter.phenotypemtcissue attribute)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcIssue.reason", false]], "reason (gpsea.analysis.mtc_filter.phenotypemtcresult property)": [[2, "gpsea.analysis.mtc_filter.PhenotypeMtcResult.reason", false]], "ref (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.ref", false]], "ref_length() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.ref_length", false]], "refseq_name (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.refseq_name", false]], "region (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Region", false]], "region (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.region", false]], "region (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.REGION", false]], "region (gpsea.model.transcriptcoordinates property)": [[15, "gpsea.model.TranscriptCoordinates.region", false]], "region (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.region", false]], "region() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.region", false]], "regions() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.regions", false]], "regulatory_region_ablation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.REGULATORY_REGION_ABLATION", false]], "regulatory_region_amplification (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.REGULATORY_REGION_AMPLIFICATION", false]], "regulatory_region_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.REGULATORY_REGION_VARIANT", false]], "repeat (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.REPEAT", false]], "repeats() (gpsea.model.proteinmetadata method)": [[15, "gpsea.model.ProteinMetadata.repeats", false]], "same_count_as_the_only_child (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SAME_COUNT_AS_THE_ONLY_CHILD", false]], "samplelabels (class in gpsea.model)": [[15, "gpsea.model.SampleLabels", false]], "score() (gpsea.analysis.pscore.countingphenotypescorer method)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.score", false]], "score() (gpsea.analysis.pscore.devriesphenotypescorer method)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.score", false]], "score() (gpsea.analysis.pscore.measurementphenotypescorer method)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.score", false]], "score() (gpsea.analysis.pscore.phenotypescorer method)": [[8, "gpsea.analysis.pscore.PhenotypeScorer.score", false]], "sequence_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SEQUENCE_VARIANT", false]], "sex (class in gpsea.model)": [[15, "gpsea.model.Sex", false]], "sex (gpsea.model.patient property)": [[15, "gpsea.model.Patient.sex", false]], "sex_predicate() (in module gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.sex_predicate", false]], "significant_phenotype_indices() (gpsea.analysis.multiphenotypeanalysisresult method)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.significant_phenotype_indices", false]], "significant_phenotype_indices() (gpsea.analysis.pcats.multiphenotypeanalysisresult method)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.significant_phenotype_indices", false]], "single() (gpsea.model.genotypes static method)": [[15, "gpsea.model.Genotypes.single", false]], "skipping_general_term (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_GENERAL_TERM", false]], "skipping_non_phenotype_term (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_NON_PHENOTYPE_TERM", false]], "skipping_since_one_genotype_had_zero_observations (gpsea.analysis.mtc_filter.hpomtcfilter attribute)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS", false]], "snv (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.SNV", false]], "some_cell_has_greater_than_one_count() (gpsea.analysis.mtc_filter.hpomtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.HpoMtcFilter.some_cell_has_greater_than_one_count", false]], "specifiedtermsmtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter", false]], "splice_acceptor_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_ACCEPTOR_VARIANT", false]], "splice_donor_5th_base_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_DONOR_5TH_BASE_VARIANT", false]], "splice_donor_region_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_DONOR_REGION_VARIANT", false]], "splice_donor_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_DONOR_VARIANT", false]], "splice_polypyrimidine_tract_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_POLYPYRIMIDINE_TRACT_VARIANT", false]], "splice_region_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SPLICE_REGION_VARIANT", false]], "start (gpsea.model.featureinfo property)": [[15, "gpsea.model.FeatureInfo.start", false]], "start (gpsea.model.genome.region property)": [[16, "gpsea.model.genome.Region.start", false]], "start (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.start", false]], "start_lost (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.START_LOST", false]], "start_on_strand() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.start_on_strand", false]], "start_retained_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.START_RETAINED_VARIANT", false]], "statistic (class in gpsea.analysis)": [[1, "gpsea.analysis.Statistic", false]], "statistic (gpsea.analysis.analysisresult property)": [[1, "gpsea.analysis.AnalysisResult.statistic", false]], "statistic (gpsea.analysis.statisticresult property)": [[1, "gpsea.analysis.StatisticResult.statistic", false]], "statistic_result() (gpsea.analysis.monophenotypeanalysisresult method)": [[1, "gpsea.analysis.MonoPhenotypeAnalysisResult.statistic_result", false]], "statistic_results (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.statistic_results", false]], "statistic_results (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.statistic_results", false]], "statisticresult (class in gpsea.analysis)": [[1, "gpsea.analysis.StatisticResult", false]], "status (class in gpsea.model)": [[15, "gpsea.model.Status", false]], "status (gpsea.model.vitalstatus attribute)": [[15, "gpsea.model.VitalStatus.status", false]], "stop_gained (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.STOP_GAINED", false]], "stop_lost (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.STOP_LOST", false]], "stop_retained_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.STOP_RETAINED_VARIANT", false]], "store_annotations() (gpsea.preprocessing.proteinannotationcache method)": [[17, "gpsea.preprocessing.ProteinAnnotationCache.store_annotations", false]], "store_annotations() (gpsea.preprocessing.variantannotationcache method)": [[17, "gpsea.preprocessing.VariantAnnotationCache.store_annotations", false]], "strand (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Strand", false]], "strand (gpsea.model.genome.genomicregion property)": [[16, "gpsea.model.genome.GenomicRegion.strand", false]], "strand (gpsea.model.genome.stranded property)": [[16, "gpsea.model.genome.Stranded.strand", false]], "stranded (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Stranded", false]], "structural_so_id_to_display() (gpsea.model.varianteffect static method)": [[15, "gpsea.model.VariantEffect.structural_so_id_to_display", false]], "structural_type (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.structural_type", false]], "structural_type() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.structural_type", false]], "summarize() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.summarize", false]], "summarize() (gpsea.preprocessing.preprocessingvalidationresult method)": [[17, "gpsea.preprocessing.PreprocessingValidationResult.summarize", false]], "summarize_groups() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.summarize_groups", false]], "summarize_hpo_analysis() (in module gpsea.view)": [[19, "gpsea.view.summarize_hpo_analysis", false]], "supports_shape (gpsea.analysis.pcats.stats.countstatistic property)": [[4, "gpsea.analysis.pcats.stats.CountStatistic.supports_shape", false]], "supports_shape (gpsea.analysis.pcats.stats.fisherexacttest property)": [[4, "gpsea.analysis.pcats.stats.FisherExactTest.supports_shape", false]], "survival (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.Survival", false]], "survivalanalysis (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.SurvivalAnalysis", false]], "survivalanalysisresult (class in gpsea.analysis.temporal)": [[10, "gpsea.analysis.temporal.SurvivalAnalysisResult", false]], "survivalstatistic (class in gpsea.analysis.temporal.stats)": [[12, "gpsea.analysis.temporal.stats.SurvivalStatistic", false]], "sv_info (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.sv_info", false]], "symbol (gpsea.model.genome.strand property)": [[16, "gpsea.model.genome.Strand.symbol", false]], "synonymous_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.SYNONYMOUS_VARIANT", false]], "term_id (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.term_id", false]], "terms_to_test (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter property)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.terms_to_test", false]], "test() (gpsea.analysis.predicate.genotype.variantpredicate method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicate.test", false]], "test() (gpsea.analysis.predicate.phenotype.diseasepresencepredicate method)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.test", false]], "test() (gpsea.analysis.predicate.phenotype.hpopredicate method)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.test", false]], "test() (gpsea.analysis.predicate.polypredicate method)": [[5, "gpsea.analysis.predicate.PolyPredicate.test", false]], "test_result (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.test_result", false]], "tf_binding_site_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TF_BINDING_SITE_VARIANT", false]], "tfbs_ablation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TFBS_ABLATION", false]], "tfbs_amplification (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TFBS_AMPLIFICATION", false]], "three_prime_utr_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.THREE_PRIME_UTR_VARIANT", false]], "timeline (class in gpsea.model)": [[15, "gpsea.model.Timeline", false]], "timeline (gpsea.model.age property)": [[15, "gpsea.model.Age.timeline", false]], "to_display() (gpsea.model.varianteffect method)": [[15, "gpsea.model.VariantEffect.to_display", false]], "to_negative_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.to_negative_strand", false]], "to_opposite_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.to_opposite_strand", false]], "to_positive_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.to_positive_strand", false]], "to_string() (gpsea.model.proteinfeature method)": [[15, "gpsea.model.ProteinFeature.to_string", false]], "total_patient_count (gpsea.model.cohort property)": [[15, "gpsea.model.Cohort.total_patient_count", false]], "total_tests (gpsea.analysis.multiphenotypeanalysisresult property)": [[1, "gpsea.analysis.MultiPhenotypeAnalysisResult.total_tests", false]], "total_tests (gpsea.analysis.pcats.multiphenotypeanalysisresult property)": [[3, "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult.total_tests", false]], "transcript() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.transcript", false]], "transcript_ablation (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TRANSCRIPT_ABLATION", false]], "transcript_amplification (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.TRANSCRIPT_AMPLIFICATION", false]], "transcript_coordinates (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.transcript_coordinates", false]], "transcript_id (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.transcript_id", false]], "transcript_id (gpsea.model.transcriptinfoaware property)": [[15, "gpsea.model.TranscriptInfoAware.transcript_id", false]], "transcript_id (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.transcript_id", false]], "transcriptannotation (class in gpsea.model)": [[15, "gpsea.model.TranscriptAnnotation", false]], "transcriptcoordinates (class in gpsea.model)": [[15, "gpsea.model.TranscriptCoordinates", false]], "transcriptcoordinateservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.TranscriptCoordinateService", false]], "transcriptinfoaware (class in gpsea.model)": [[15, "gpsea.model.TranscriptInfoAware", false]], "translocation (gpsea.model.variantclass attribute)": [[15, "gpsea.model.VariantClass.TRANSLOCATION", false]], "transposable (class in gpsea.model.genome)": [[16, "gpsea.model.genome.Transposable", false]], "transpose_coordinate() (in module gpsea.model.genome)": [[16, "gpsea.model.genome.transpose_coordinate", false]], "true() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.true", false]], "tteststatistic (class in gpsea.analysis.pscore.stats)": [[9, "gpsea.analysis.pscore.stats.TTestStatistic", false]], "tx_annotations (gpsea.model.functionalannotationaware property)": [[15, "gpsea.model.FunctionalAnnotationAware.tx_annotations", false]], "tx_annotations (gpsea.model.variant property)": [[15, "gpsea.model.Variant.tx_annotations", false]], "ucsc_name (gpsea.model.genome.contig property)": [[16, "gpsea.model.genome.Contig.ucsc_name", false]], "uniprotproteinmetadataservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.UniprotProteinMetadataService", false]], "unit (gpsea.model.measurement property)": [[15, "gpsea.model.Measurement.unit", false]], "unknown (gpsea.model.status attribute)": [[15, "gpsea.model.Status.UNKNOWN", false]], "unknown_sex (gpsea.model.sex attribute)": [[15, "gpsea.model.Sex.UNKNOWN_SEX", false]], "upstream_gene_variant (gpsea.model.varianteffect attribute)": [[15, "gpsea.model.VariantEffect.UPSTREAM_GENE_VARIANT", false]], "usealltermsmtcfilter (class in gpsea.analysis.mtc_filter)": [[2, "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter", false]], "value (gpsea.analysis.temporal.survival attribute)": [[10, "gpsea.analysis.temporal.Survival.value", false]], "varcachingfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VarCachingFunctionalAnnotator", false]], "variable_name (gpsea.analysis.predicate.phenotype.diseasepresencepredicate property)": [[7, "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate.variable_name", false]], "variable_name (gpsea.analysis.predicate.phenotype.hpopredicate property)": [[7, "gpsea.analysis.predicate.phenotype.HpoPredicate.variable_name", false]], "variable_name (gpsea.analysis.pscore.countingphenotypescorer property)": [[8, "gpsea.analysis.pscore.CountingPhenotypeScorer.variable_name", false]], "variable_name (gpsea.analysis.pscore.devriesphenotypescorer property)": [[8, "gpsea.analysis.pscore.DeVriesPhenotypeScorer.variable_name", false]], "variable_name (gpsea.analysis.pscore.measurementphenotypescorer property)": [[8, "gpsea.analysis.pscore.MeasurementPhenotypeScorer.variable_name", false]], "variant (class in gpsea.model)": [[15, "gpsea.model.Variant", false]], "variant_class (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.variant_class", false]], "variant_class (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.variant_class", false]], "variant_class (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.variant_class", false]], "variant_class() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.variant_class", false]], "variant_coordinates (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.variant_coordinates", false]], "variant_effect() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.variant_effect", false]], "variant_effect_count_by_tx() (gpsea.model.cohort method)": [[15, "gpsea.model.Cohort.variant_effect_count_by_tx", false]], "variant_effects (gpsea.model.transcriptannotation property)": [[15, "gpsea.model.TranscriptAnnotation.variant_effects", false]], "variant_effects (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.variant_effects", false]], "variant_info (gpsea.model.variant property)": [[15, "gpsea.model.Variant.variant_info", false]], "variant_info (gpsea.model.variantinfoaware property)": [[15, "gpsea.model.VariantInfoAware.variant_info", false]], "variant_key (gpsea.model.imprecisesvinfo property)": [[15, "gpsea.model.ImpreciseSvInfo.variant_key", false]], "variant_key (gpsea.model.variantcoordinates property)": [[15, "gpsea.model.VariantCoordinates.variant_key", false]], "variant_key (gpsea.model.variantinfo property)": [[15, "gpsea.model.VariantInfo.variant_key", false]], "variant_key() (gpsea.analysis.predicate.genotype.variantpredicates static method)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates.variant_key", false]], "variant_locations (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.variant_locations", false]], "variant_locations_counted_absolute (gpsea.view.proteinvisualizable property)": [[19, "gpsea.view.ProteinVisualizable.variant_locations_counted_absolute", false]], "variantannotationcache (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VariantAnnotationCache", false]], "variantclass (class in gpsea.model)": [[15, "gpsea.model.VariantClass", false]], "variantcoordinatefinder (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VariantCoordinateFinder", false]], "variantcoordinates (class in gpsea.model)": [[15, "gpsea.model.VariantCoordinates", false]], "varianteffect (class in gpsea.model)": [[15, "gpsea.model.VariantEffect", false]], "variantformatter (class in gpsea.view)": [[19, "gpsea.view.VariantFormatter", false]], "variantinfo (class in gpsea.model)": [[15, "gpsea.model.VariantInfo", false]], "variantinfoaware (class in gpsea.model)": [[15, "gpsea.model.VariantInfoAware", false]], "variantpredicate (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicate", false]], "variantpredicates (class in gpsea.analysis.predicate.genotype)": [[6, "gpsea.analysis.predicate.genotype.VariantPredicates", false]], "variants (gpsea.model.patient property)": [[15, "gpsea.model.Patient.variants", false]], "varianttranscriptvisualizer (class in gpsea.view)": [[19, "gpsea.view.VariantTranscriptVisualizer", false]], "vepfunctionalannotator (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VepFunctionalAnnotator", false]], "verify_term_id() (gpsea.analysis.mtc_filter.specifiedtermsmtcfilter static method)": [[2, "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter.verify_term_id", false]], "vital_status (gpsea.model.patient property)": [[15, "gpsea.model.Patient.vital_status", false]], "vitalstatus (class in gpsea.model)": [[15, "gpsea.model.VitalStatus", false]], "vvhgvsvariantcoordinatefinder (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VVHgvsVariantCoordinateFinder", false]], "vvmulticoordinateservice (class in gpsea.preprocessing)": [[17, "gpsea.preprocessing.VVMultiCoordinateService", false]], "with_cache_folder() (gpsea.preprocessing.varcachingfunctionalannotator static method)": [[17, "gpsea.preprocessing.VarCachingFunctionalAnnotator.with_cache_folder", false]], "with_strand() (gpsea.model.genome.genomicregion method)": [[16, "gpsea.model.genome.GenomicRegion.with_strand", false]], "with_strand() (gpsea.model.genome.transposable method)": [[16, "gpsea.model.genome.Transposable.with_strand", false]], "wrap_scoring_function() (gpsea.analysis.pscore.phenotypescorer static method)": [[8, "gpsea.analysis.pscore.PhenotypeScorer.wrap_scoring_function", false]], "write() (gpsea.view.gpseareport method)": [[19, "gpsea.view.GpseaReport.write", false]], "zinc_finger (gpsea.model.featuretype attribute)": [[15, "gpsea.model.FeatureType.ZINC_FINGER", false]]}, "objects": {"": [[0, 0, 0, "-", "gpsea"]], "gpsea": [[1, 0, 0, "-", "analysis"], [13, 0, 0, "-", "config"], [14, 0, 0, "-", "io"], [15, 0, 0, "-", "model"], [17, 0, 0, "-", "preprocessing"], [18, 0, 0, "-", "util"], [19, 0, 0, "-", "view"]], "gpsea.analysis": [[1, 1, 1, "", "AnalysisResult"], [1, 1, 1, "", "MonoPhenotypeAnalysisResult"], [1, 1, 1, "", "MultiPhenotypeAnalysisResult"], [1, 1, 1, "", "Statistic"], [1, 1, 1, "", "StatisticResult"], [2, 0, 0, "-", "mtc_filter"], [3, 0, 0, "-", "pcats"], [5, 0, 0, "-", "predicate"], [8, 0, 0, "-", "pscore"], [10, 0, 0, "-", "temporal"]], "gpsea.analysis.AnalysisResult": [[1, 2, 1, "", "gt_predicate"], [1, 2, 1, "", "statistic"]], "gpsea.analysis.MonoPhenotypeAnalysisResult": [[1, 3, 1, "", "DATA_COLUMNS"], [1, 3, 1, "", "GT_COL"], [1, 3, 1, "", "PH_COL"], [1, 4, 1, "", "complete_records"], [1, 2, 1, "", "data"], [1, 2, 1, "", "phenotype"], [1, 2, 1, "", "pval"], [1, 4, 1, "", "statistic_result"]], "gpsea.analysis.MultiPhenotypeAnalysisResult": [[1, 2, 1, "", "all_counts"], [1, 2, 1, "", "corrected_pvals"], [1, 2, 1, "", "mtc_correction"], [1, 4, 1, "", "n_significant_for_alpha"], [1, 2, 1, "", "n_usable"], [1, 2, 1, "", "pheno_predicates"], [1, 2, 1, "", "phenotypes"], [1, 2, 1, "", "pvals"], [1, 4, 1, "", "significant_phenotype_indices"], [1, 2, 1, "", "statistic_results"], [1, 2, 1, "", "total_tests"]], "gpsea.analysis.Statistic": [[1, 2, 1, "", "name"]], "gpsea.analysis.StatisticResult": [[1, 2, 1, "", "pval"], [1, 2, 1, "", "statistic"]], "gpsea.analysis.mtc_filter": [[2, 1, 1, "", "HpoMtcFilter"], [2, 1, 1, "", "PhenotypeMtcFilter"], [2, 1, 1, "", "PhenotypeMtcIssue"], [2, 1, 1, "", "PhenotypeMtcResult"], [2, 1, 1, "", "SpecifiedTermsMtcFilter"], [2, 1, 1, "", "UseAllTermsMtcFilter"]], "gpsea.analysis.mtc_filter.HpoMtcFilter": [[2, 3, 1, "", "NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO"], [2, 3, 1, "", "SAME_COUNT_AS_THE_ONLY_CHILD"], [2, 3, 1, "", "SKIPPING_GENERAL_TERM"], [2, 3, 1, "", "SKIPPING_NON_PHENOTYPE_TERM"], [2, 3, 1, "", "SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS"], [2, 4, 1, "", "default_filter"], [2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "get_maximum_group_observed_HPO_frequency"], [2, 4, 1, "", "get_number_of_observed_hpo_observations"], [2, 4, 1, "", "one_genotype_has_zero_hpo_observations"], [2, 4, 1, "", "possible_results"], [2, 4, 1, "", "some_cell_has_greater_than_one_count"]], "gpsea.analysis.mtc_filter.PhenotypeMtcFilter": [[2, 3, 1, "", "OK"], [2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "possible_results"]], "gpsea.analysis.mtc_filter.PhenotypeMtcIssue": [[2, 3, 1, "", "code"], [2, 3, 1, "", "reason"]], "gpsea.analysis.mtc_filter.PhenotypeMtcResult": [[2, 4, 1, "", "fail"], [2, 4, 1, "", "is_filtered_out"], [2, 4, 1, "", "is_passed"], [2, 2, 1, "", "mtc_issue"], [2, 4, 1, "", "ok"], [2, 2, 1, "", "reason"]], "gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter": [[2, 3, 1, "", "NON_SPECIFIED_TERM"], [2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "possible_results"], [2, 2, 1, "", "terms_to_test"], [2, 4, 1, "", "verify_term_id"]], "gpsea.analysis.mtc_filter.UseAllTermsMtcFilter": [[2, 4, 1, "", "filter"], [2, 4, 1, "", "filter_method_name"], [2, 4, 1, "", "possible_results"]], "gpsea.analysis.pcats": [[3, 1, 1, "", "DiseaseAnalysis"], [3, 1, 1, "", "HpoTermAnalysis"], [3, 1, 1, "", "HpoTermAnalysisResult"], [3, 1, 1, "", "MultiPhenotypeAnalysis"], [3, 1, 1, "", "MultiPhenotypeAnalysisResult"], [3, 5, 1, "", "apply_predicates_on_patients"], [3, 5, 1, "", "configure_hpo_term_analysis"], [4, 0, 0, "-", "stats"]], "gpsea.analysis.pcats.HpoTermAnalysisResult": [[3, 2, 1, "", "mtc_filter_name"], [3, 2, 1, "", "mtc_filter_results"], [3, 4, 1, "", "n_filtered_out"]], "gpsea.analysis.pcats.MultiPhenotypeAnalysis": [[3, 4, 1, "", "compare_genotype_vs_phenotypes"]], "gpsea.analysis.pcats.MultiPhenotypeAnalysisResult": [[3, 2, 1, "", "all_counts"], [3, 2, 1, "", "corrected_pvals"], [3, 2, 1, "", "mtc_correction"], [3, 4, 1, "", "n_significant_for_alpha"], [3, 2, 1, "", "n_usable"], [3, 2, 1, "", "pheno_predicates"], [3, 2, 1, "", "phenotypes"], [3, 2, 1, "", "pvals"], [3, 4, 1, "", "significant_phenotype_indices"], [3, 2, 1, "", "statistic_results"], [3, 2, 1, "", "total_tests"]], "gpsea.analysis.pcats.stats": [[4, 1, 1, "", "CountStatistic"], [4, 1, 1, "", "FisherExactTest"]], "gpsea.analysis.pcats.stats.CountStatistic": [[4, 4, 1, "", "compute_pval"], [4, 2, 1, "", "supports_shape"]], "gpsea.analysis.pcats.stats.FisherExactTest": [[4, 4, 1, "", "compute_pval"], [4, 2, 1, "", "supports_shape"]], "gpsea.analysis.predicate": [[5, 1, 1, "", "PolyPredicate"], [6, 0, 0, "-", "genotype"], [7, 0, 0, "-", "phenotype"]], "gpsea.analysis.predicate.PolyPredicate": [[5, 4, 1, "", "get_categories"], [5, 4, 1, "", "get_categorizations"], [5, 4, 1, "", "get_category"], [5, 4, 1, "", "get_category_name"], [5, 2, 1, "", "group_labels"], [5, 4, 1, "", "n_categorizations"], [5, 4, 1, "", "summarize"], [5, 4, 1, "", "summarize_groups"], [5, 4, 1, "", "test"]], "gpsea.analysis.predicate.genotype": [[6, 1, 1, "", "AlleleCounter"], [6, 1, 1, "", "GenotypePolyPredicate"], [6, 1, 1, "", "VariantPredicate"], [6, 1, 1, "", "VariantPredicates"], [6, 5, 1, "", "allele_count"], [6, 5, 1, "", "biallelic_predicate"], [6, 5, 1, "", "diagnosis_predicate"], [6, 5, 1, "", "monoallelic_predicate"], [6, 5, 1, "", "sex_predicate"]], "gpsea.analysis.predicate.genotype.AlleleCounter": [[6, 4, 1, "", "count"], [6, 4, 1, "", "get_question"]], "gpsea.analysis.predicate.genotype.VariantPredicate": [[6, 4, 1, "", "get_question"], [6, 4, 1, "", "test"]], "gpsea.analysis.predicate.genotype.VariantPredicates": [[6, 4, 1, "", "all"], [6, 4, 1, "", "any"], [6, 4, 1, "", "change_length"], [6, 4, 1, "", "exon"], [6, 4, 1, "", "gene"], [6, 4, 1, "", "is_large_imprecise_sv"], [6, 4, 1, "", "is_structural_deletion"], [6, 4, 1, "", "is_structural_variant"], [6, 4, 1, "", "protein_feature"], [6, 4, 1, "", "protein_feature_type"], [6, 4, 1, "", "ref_length"], [6, 4, 1, "", "region"], [6, 4, 1, "", "structural_type"], [6, 4, 1, "", "transcript"], [6, 4, 1, "", "true"], [6, 4, 1, "", "variant_class"], [6, 4, 1, "", "variant_effect"], [6, 4, 1, "", "variant_key"]], "gpsea.analysis.predicate.phenotype": [[7, 1, 1, "", "DiseasePresencePredicate"], [7, 1, 1, "", "HpoPredicate"], [7, 1, 1, "", "PhenotypeCategorization"], [7, 1, 1, "", "PhenotypePolyPredicate"], [7, 5, 1, "", "prepare_hpo_terms_of_interest"], [7, 5, 1, "", "prepare_predicates_for_terms_of_interest"]], "gpsea.analysis.predicate.phenotype.DiseasePresencePredicate": [[7, 2, 1, "", "description"], [7, 4, 1, "", "get_categorizations"], [7, 2, 1, "", "name"], [7, 2, 1, "", "phenotype"], [7, 2, 1, "", "present_phenotype_categorization"], [7, 4, 1, "", "test"], [7, 2, 1, "", "variable_name"]], "gpsea.analysis.predicate.phenotype.HpoPredicate": [[7, 2, 1, "", "description"], [7, 4, 1, "", "get_categorizations"], [7, 2, 1, "", "name"], [7, 2, 1, "", "phenotype"], [7, 2, 1, "", "present_phenotype_categorization"], [7, 4, 1, "", "test"], [7, 2, 1, "", "variable_name"]], "gpsea.analysis.predicate.phenotype.PhenotypeCategorization": [[7, 2, 1, "", "phenotype"]], "gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate": [[7, 2, 1, "", "phenotype"], [7, 2, 1, "", "present_phenotype_categorization"], [7, 2, 1, "", "present_phenotype_category"]], "gpsea.analysis.pscore": [[8, 1, 1, "", "CountingPhenotypeScorer"], [8, 1, 1, "", "DeVriesPhenotypeScorer"], [8, 1, 1, "", "MeasurementPhenotypeScorer"], [8, 1, 1, "", "PhenotypeScoreAnalysis"], [8, 1, 1, "", "PhenotypeScoreAnalysisResult"], [8, 1, 1, "", "PhenotypeScorer"], [9, 0, 0, "-", "stats"]], "gpsea.analysis.pscore.CountingPhenotypeScorer": [[8, 2, 1, "", "description"], [8, 4, 1, "", "from_query_curies"], [8, 2, 1, "", "name"], [8, 4, 1, "", "score"], [8, 2, 1, "", "variable_name"]], "gpsea.analysis.pscore.DeVriesPhenotypeScorer": [[8, 2, 1, "", "description"], [8, 2, 1, "", "name"], [8, 4, 1, "", "score"], [8, 2, 1, "", "variable_name"]], "gpsea.analysis.pscore.MeasurementPhenotypeScorer": [[8, 2, 1, "", "description"], [8, 4, 1, "", "from_measurement_id"], [8, 2, 1, "", "label"], [8, 2, 1, "", "name"], [8, 4, 1, "", "score"], [8, 2, 1, "", "term_id"], [8, 2, 1, "", "variable_name"]], "gpsea.analysis.pscore.PhenotypeScoreAnalysis": [[8, 4, 1, "", "compare_genotype_vs_phenotype_score"]], "gpsea.analysis.pscore.PhenotypeScoreAnalysisResult": [[8, 4, 1, "", "phenotype_scorer"], [8, 4, 1, "", "plot_boxplots"]], "gpsea.analysis.pscore.PhenotypeScorer": [[8, 4, 1, "", "score"], [8, 4, 1, "", "wrap_scoring_function"]], "gpsea.analysis.pscore.stats": [[9, 1, 1, "", "MannWhitneyStatistic"], [9, 1, 1, "", "PhenotypeScoreStatistic"], [9, 1, 1, "", "TTestStatistic"]], "gpsea.analysis.pscore.stats.MannWhitneyStatistic": [[9, 4, 1, "", "compute_pval"]], "gpsea.analysis.pscore.stats.PhenotypeScoreStatistic": [[9, 4, 1, "", "compute_pval"]], "gpsea.analysis.pscore.stats.TTestStatistic": [[9, 4, 1, "", "compute_pval"]], "gpsea.analysis.temporal": [[10, 1, 1, "", "Endpoint"], [10, 1, 1, "", "Survival"], [10, 1, 1, "", "SurvivalAnalysis"], [10, 1, 1, "", "SurvivalAnalysisResult"], [11, 0, 0, "-", "endpoint"], [12, 0, 0, "-", "stats"]], "gpsea.analysis.temporal.Endpoint": [[10, 4, 1, "", "compute_survival"]], "gpsea.analysis.temporal.Survival": [[10, 3, 1, "", "is_censored"], [10, 3, 1, "", "value"]], "gpsea.analysis.temporal.SurvivalAnalysis": [[10, 4, 1, "", "compare_genotype_vs_survival"]], "gpsea.analysis.temporal.SurvivalAnalysisResult": [[10, 2, 1, "", "endpoint"], [10, 4, 1, "", "plot_kaplan_meier_curves"]], "gpsea.analysis.temporal.endpoint": [[11, 5, 1, "", "death"], [11, 5, 1, "", "disease_onset"], [11, 5, 1, "", "hpo_onset"]], "gpsea.analysis.temporal.stats": [[12, 1, 1, "", "LogRankTest"], [12, 1, 1, "", "SurvivalStatistic"]], "gpsea.analysis.temporal.stats.LogRankTest": [[12, 4, 1, "", "compute_pval"]], "gpsea.analysis.temporal.stats.SurvivalStatistic": [[12, 4, 1, "", "compute_pval"]], "gpsea.config": [[13, 6, 1, "", "CACHE_ENV"], [13, 6, 1, "", "DEFAULT_CACHE_PATH"], [13, 5, 1, "", "get_cache_dir_path"]], "gpsea.io": [[14, 1, 1, "", "GpseaJSONDecoder"], [14, 1, 1, "", "GpseaJSONEncoder"]], "gpsea.io.GpseaJSONDecoder": [[14, 4, 1, "", "object_hook"]], "gpsea.io.GpseaJSONEncoder": [[14, 4, 1, "", "default"]], "gpsea.model": [[15, 1, 1, "", "Age"], [15, 1, 1, "", "Cohort"], [15, 1, 1, "", "Disease"], [15, 1, 1, "", "FeatureInfo"], [15, 1, 1, "", "FeatureType"], [15, 1, 1, "", "FunctionalAnnotationAware"], [15, 1, 1, "", "Genotype"], [15, 1, 1, "", "Genotyped"], [15, 1, 1, "", "Genotypes"], [15, 1, 1, "", "ImpreciseSvInfo"], [15, 1, 1, "", "Measurement"], [15, 1, 1, "", "Patient"], [15, 1, 1, "", "Phenotype"], [15, 1, 1, "", "ProteinFeature"], [15, 1, 1, "", "ProteinMetadata"], [15, 1, 1, "", "SampleLabels"], [15, 1, 1, "", "Sex"], [15, 1, 1, "", "Status"], [15, 1, 1, "", "Timeline"], [15, 1, 1, "", "TranscriptAnnotation"], [15, 1, 1, "", "TranscriptCoordinates"], [15, 1, 1, "", "TranscriptInfoAware"], [15, 1, 1, "", "Variant"], [15, 1, 1, "", "VariantClass"], [15, 1, 1, "", "VariantCoordinates"], [15, 1, 1, "", "VariantEffect"], [15, 1, 1, "", "VariantInfo"], [15, 1, 1, "", "VariantInfoAware"], [15, 1, 1, "", "VitalStatus"], [16, 0, 0, "-", "genome"]], "gpsea.model.Age": [[15, 3, 1, "", "DAYS_IN_MONTH"], [15, 3, 1, "", "DAYS_IN_WEEK"], [15, 3, 1, "", "DAYS_IN_YEAR"], [15, 3, 1, "", "ISO8601PT"], [15, 4, 1, "", "birth"], [15, 2, 1, "", "days"], [15, 4, 1, "", "from_iso8601_period"], [15, 4, 1, "", "gestational"], [15, 4, 1, "", "gestational_days"], [15, 2, 1, "", "is_gestational"], [15, 2, 1, "", "is_postnatal"], [15, 4, 1, "", "last_menstrual_period"], [15, 4, 1, "", "postnatal"], [15, 4, 1, "", "postnatal_days"], [15, 4, 1, "", "postnatal_years"], [15, 2, 1, "", "timeline"]], "gpsea.model.Cohort": [[15, 4, 1, "", "all_diseases"], [15, 4, 1, "", "all_measurements"], [15, 2, 1, "", "all_patients"], [15, 4, 1, "", "all_phenotypes"], [15, 2, 1, "", "all_transcript_ids"], [15, 4, 1, "", "all_variant_infos"], [15, 4, 1, "", "all_variants"], [15, 4, 1, "", "count_alive"], [15, 4, 1, "", "count_deceased"], [15, 4, 1, "", "count_distinct_diseases"], [15, 4, 1, "", "count_distinct_hpo_terms"], [15, 4, 1, "", "count_distinct_measurements"], [15, 4, 1, "", "count_females"], [15, 4, 1, "", "count_males"], [15, 4, 1, "", "count_unknown_sex"], [15, 4, 1, "", "count_unknown_vital_status"], [15, 4, 1, "", "count_with_age_of_last_encounter"], [15, 4, 1, "", "count_with_disease_onset"], [15, 4, 1, "", "from_patients"], [15, 4, 1, "", "get_excluded_count"], [15, 4, 1, "", "get_patient_ids"], [15, 4, 1, "", "get_variant_by_key"], [15, 4, 1, "", "list_all_diseases"], [15, 4, 1, "", "list_all_proteins"], [15, 4, 1, "", "list_all_variants"], [15, 4, 1, "", "list_measurements"], [15, 4, 1, "", "list_present_phenotypes"], [15, 2, 1, "", "total_patient_count"], [15, 4, 1, "", "variant_effect_count_by_tx"]], "gpsea.model.Disease": [[15, 4, 1, "", "from_raw_parts"], [15, 2, 1, "", "identifier"], [15, 2, 1, "", "is_present"], [15, 2, 1, "", "name"], [15, 2, 1, "", "onset"]], "gpsea.model.FeatureInfo": [[15, 2, 1, "", "end"], [15, 2, 1, "", "name"], [15, 4, 1, "", "overlaps_with"], [15, 2, 1, "", "region"], [15, 2, 1, "", "start"]], "gpsea.model.FeatureType": [[15, 3, 1, "", "COILED_COIL"], [15, 3, 1, "", "COMPOSITIONAL_BIAS"], [15, 3, 1, "", "DOMAIN"], [15, 3, 1, "", "MOTIF"], [15, 3, 1, "", "REGION"], [15, 3, 1, "", "REPEAT"], [15, 3, 1, "", "ZINC_FINGER"], [15, 4, 1, "", "from_string"]], "gpsea.model.FunctionalAnnotationAware": [[15, 4, 1, "", "get_hgvs_cdna_by_tx_id"], [15, 4, 1, "", "get_preferred_tx_annotation"], [15, 4, 1, "", "get_tx_anno_by_tx_id"], [15, 2, 1, "", "tx_annotations"]], "gpsea.model.Genotype": [[15, 3, 1, "", "HEMIZYGOUS"], [15, 3, 1, "", "HETEROZYGOUS"], [15, 3, 1, "", "HOMOZYGOUS_ALTERNATE"], [15, 3, 1, "", "HOMOZYGOUS_REFERENCE"], [15, 3, 1, "", "NO_CALL"], [15, 2, 1, "", "code"]], "gpsea.model.Genotyped": [[15, 4, 1, "", "genotype_for_sample"], [15, 2, 1, "", "genotypes"]], "gpsea.model.Genotypes": [[15, 4, 1, "", "empty"], [15, 4, 1, "", "for_sample"], [15, 4, 1, "", "from_mapping"], [15, 4, 1, "", "single"]], "gpsea.model.ImpreciseSvInfo": [[15, 2, 1, "", "gene_id"], [15, 2, 1, "", "gene_symbol"], [15, 2, 1, "", "structural_type"], [15, 2, 1, "", "variant_class"], [15, 2, 1, "", "variant_key"]], "gpsea.model.Measurement": [[15, 2, 1, "", "identifier"], [15, 2, 1, "", "name"], [15, 2, 1, "", "test_result"], [15, 2, 1, "", "unit"]], "gpsea.model.Patient": [[15, 2, 1, "", "age"], [15, 4, 1, "", "count_unique_diseases"], [15, 4, 1, "", "count_unique_measurements"], [15, 4, 1, "", "count_unique_phenotypes"], [15, 4, 1, "", "disease_by_id"], [15, 2, 1, "", "diseases"], [15, 4, 1, "", "excluded_diseases"], [15, 4, 1, "", "excluded_phenotypes"], [15, 4, 1, "", "from_raw_parts"], [15, 2, 1, "", "labels"], [15, 4, 1, "", "measurement_by_id"], [15, 2, 1, "", "measurements"], [15, 2, 1, "", "patient_id"], [15, 4, 1, "", "phenotype_by_id"], [15, 2, 1, "", "phenotypes"], [15, 4, 1, "", "present_diseases"], [15, 4, 1, "", "present_phenotypes"], [15, 2, 1, "", "sex"], [15, 2, 1, "", "variants"], [15, 2, 1, "", "vital_status"]], "gpsea.model.Phenotype": [[15, 4, 1, "", "from_raw_parts"], [15, 4, 1, "", "from_term"], [15, 2, 1, "", "identifier"], [15, 2, 1, "", "is_observed"], [15, 2, 1, "", "is_present"], [15, 2, 1, "", "observed"], [15, 2, 1, "", "onset"]], "gpsea.model.ProteinFeature": [[15, 4, 1, "", "create"], [15, 2, 1, "", "feature_type"], [15, 2, 1, "", "info"], [15, 4, 1, "", "to_string"]], "gpsea.model.ProteinMetadata": [[15, 4, 1, "", "domains"], [15, 4, 1, "", "from_feature_frame"], [15, 4, 1, "", "from_uniprot_json"], [15, 4, 1, "", "get_features_variant_overlaps"], [15, 2, 1, "", "label"], [15, 4, 1, "", "motifs"], [15, 2, 1, "", "protein_features"], [15, 2, 1, "", "protein_id"], [15, 2, 1, "", "protein_length"], [15, 4, 1, "", "regions"], [15, 4, 1, "", "repeats"]], "gpsea.model.SampleLabels": [[15, 2, 1, "", "label"], [15, 4, 1, "", "label_summary"], [15, 2, 1, "", "meta_label"]], "gpsea.model.Sex": [[15, 3, 1, "", "FEMALE"], [15, 3, 1, "", "MALE"], [15, 3, 1, "", "UNKNOWN_SEX"], [15, 4, 1, "", "is_female"], [15, 4, 1, "", "is_male"], [15, 4, 1, "", "is_provided"], [15, 4, 1, "", "is_unknown"]], "gpsea.model.Status": [[15, 3, 1, "", "ALIVE"], [15, 3, 1, "", "DECEASED"], [15, 3, 1, "", "UNKNOWN"]], "gpsea.model.Timeline": [[15, 3, 1, "", "GESTATIONAL"], [15, 3, 1, "", "POSTNATAL"]], "gpsea.model.TranscriptAnnotation": [[15, 2, 1, "", "gene_id"], [15, 2, 1, "", "hgvs_cdna"], [15, 2, 1, "", "hgvsp"], [15, 2, 1, "", "is_preferred"], [15, 2, 1, "", "overlapping_exons"], [15, 2, 1, "", "protein_effect_location"], [15, 2, 1, "", "protein_id"], [15, 2, 1, "", "transcript_id"], [15, 2, 1, "", "variant_effects"]], "gpsea.model.TranscriptCoordinates": [[15, 2, 1, "", "cds_end"], [15, 2, 1, "", "cds_start"], [15, 2, 1, "", "exons"], [15, 4, 1, "", "get_cds_regions"], [15, 4, 1, "", "get_coding_base_count"], [15, 4, 1, "", "get_codon_count"], [15, 4, 1, "", "get_five_prime_utrs"], [15, 4, 1, "", "get_three_prime_utrs"], [15, 2, 1, "", "identifier"], [15, 4, 1, "", "is_coding"], [15, 2, 1, "", "is_preferred"], [15, 2, 1, "", "region"]], "gpsea.model.TranscriptInfoAware": [[15, 2, 1, "", "gene_id"], [15, 2, 1, "", "transcript_id"]], "gpsea.model.Variant": [[15, 4, 1, "", "create_variant_from_scratch"], [15, 2, 1, "", "genotypes"], [15, 2, 1, "", "tx_annotations"], [15, 2, 1, "", "variant_info"]], "gpsea.model.VariantClass": [[15, 3, 1, "", "DEL"], [15, 3, 1, "", "DUP"], [15, 3, 1, "", "INS"], [15, 3, 1, "", "INV"], [15, 3, 1, "", "MNV"], [15, 3, 1, "", "SNV"], [15, 3, 1, "", "TRANSLOCATION"]], "gpsea.model.VariantCoordinates": [[15, 2, 1, "", "alt"], [15, 2, 1, "", "change_length"], [15, 2, 1, "", "chrom"], [15, 2, 1, "", "end"], [15, 4, 1, "", "from_vcf_literal"], [15, 4, 1, "", "from_vcf_symbolic"], [15, 4, 1, "", "is_structural"], [15, 2, 1, "", "ref"], [15, 2, 1, "", "region"], [15, 2, 1, "", "start"], [15, 2, 1, "", "variant_class"], [15, 2, 1, "", "variant_key"]], "gpsea.model.VariantEffect": [[15, 3, 1, "", "CODING_SEQUENCE_VARIANT"], [15, 3, 1, "", "DOWNSTREAM_GENE_VARIANT"], [15, 3, 1, "", "FEATURE_ELONGATION"], [15, 3, 1, "", "FEATURE_TRUNCATION"], [15, 3, 1, "", "FIVE_PRIME_UTR_VARIANT"], [15, 3, 1, "", "FRAMESHIFT_VARIANT"], [15, 3, 1, "", "INCOMPLETE_TERMINAL_CODON_VARIANT"], [15, 3, 1, "", "INFRAME_DELETION"], [15, 3, 1, "", "INFRAME_INSERTION"], [15, 3, 1, "", "INTERGENIC_VARIANT"], [15, 3, 1, "", "INTRON_VARIANT"], [15, 3, 1, "", "MATURE_MIRNA_VARIANT"], [15, 3, 1, "", "MISSENSE_VARIANT"], [15, 3, 1, "", "NMD_TRANSCRIPT_VARIANT"], [15, 3, 1, "", "NON_CODING_TRANSCRIPT_EXON_VARIANT"], [15, 3, 1, "", "NON_CODING_TRANSCRIPT_VARIANT"], [15, 3, 1, "", "PROTEIN_ALTERING_VARIANT"], [15, 3, 1, "", "REGULATORY_REGION_ABLATION"], [15, 3, 1, "", "REGULATORY_REGION_AMPLIFICATION"], [15, 3, 1, "", "REGULATORY_REGION_VARIANT"], [15, 3, 1, "", "SEQUENCE_VARIANT"], [15, 3, 1, "", "SPLICE_ACCEPTOR_VARIANT"], [15, 3, 1, "", "SPLICE_DONOR_5TH_BASE_VARIANT"], [15, 3, 1, "", "SPLICE_DONOR_REGION_VARIANT"], [15, 3, 1, "", "SPLICE_DONOR_VARIANT"], [15, 3, 1, "", "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"], [15, 3, 1, "", "SPLICE_REGION_VARIANT"], [15, 3, 1, "", "START_LOST"], [15, 3, 1, "", "START_RETAINED_VARIANT"], [15, 3, 1, "", "STOP_GAINED"], [15, 3, 1, "", "STOP_LOST"], [15, 3, 1, "", "STOP_RETAINED_VARIANT"], [15, 3, 1, "", "SYNONYMOUS_VARIANT"], [15, 3, 1, "", "TFBS_ABLATION"], [15, 3, 1, "", "TFBS_AMPLIFICATION"], [15, 3, 1, "", "TF_BINDING_SITE_VARIANT"], [15, 3, 1, "", "THREE_PRIME_UTR_VARIANT"], [15, 3, 1, "", "TRANSCRIPT_ABLATION"], [15, 3, 1, "", "TRANSCRIPT_AMPLIFICATION"], [15, 3, 1, "", "UPSTREAM_GENE_VARIANT"], [15, 2, 1, "", "curie"], [15, 4, 1, "", "structural_so_id_to_display"], [15, 4, 1, "", "to_display"]], "gpsea.model.VariantInfo": [[15, 4, 1, "", "has_sv_info"], [15, 4, 1, "", "has_variant_coordinates"], [15, 4, 1, "", "is_structural"], [15, 2, 1, "", "sv_info"], [15, 2, 1, "", "variant_class"], [15, 2, 1, "", "variant_coordinates"], [15, 2, 1, "", "variant_key"]], "gpsea.model.VariantInfoAware": [[15, 2, 1, "", "variant_info"]], "gpsea.model.VitalStatus": [[15, 3, 1, "", "age_of_death"], [15, 2, 1, "", "is_alive"], [15, 2, 1, "", "is_deceased"], [15, 2, 1, "", "is_unknown"], [15, 3, 1, "", "status"]], "gpsea.model.genome": [[16, 1, 1, "", "Contig"], [16, 1, 1, "", "GenomeBuild"], [16, 1, 1, "", "GenomeBuildIdentifier"], [16, 1, 1, "", "GenomicRegion"], [16, 1, 1, "", "Region"], [16, 1, 1, "", "Strand"], [16, 1, 1, "", "Stranded"], [16, 1, 1, "", "Transposable"], [16, 5, 1, "", "transpose_coordinate"]], "gpsea.model.genome.Contig": [[16, 2, 1, "", "genbank_acc"], [16, 2, 1, "", "name"], [16, 2, 1, "", "refseq_name"], [16, 2, 1, "", "ucsc_name"]], "gpsea.model.genome.GenomeBuild": [[16, 4, 1, "", "contig_by_name"], [16, 2, 1, "", "contigs"], [16, 2, 1, "", "genome_build_id"], [16, 2, 1, "", "identifier"]], "gpsea.model.genome.GenomeBuildIdentifier": [[16, 2, 1, "", "identifier"], [16, 2, 1, "", "major_assembly"], [16, 2, 1, "", "patch"]], "gpsea.model.genome.GenomicRegion": [[16, 4, 1, "", "contains"], [16, 2, 1, "", "contig"], [16, 4, 1, "", "distance_to"], [16, 4, 1, "", "end_on_strand"], [16, 4, 1, "", "overlaps_with"], [16, 4, 1, "", "start_on_strand"], [16, 2, 1, "", "strand"], [16, 4, 1, "", "with_strand"]], "gpsea.model.genome.Region": [[16, 4, 1, "", "contains"], [16, 4, 1, "", "contains_pos"], [16, 4, 1, "", "distance_to"], [16, 2, 1, "", "end"], [16, 4, 1, "", "is_empty"], [16, 4, 1, "", "overlaps_with"], [16, 2, 1, "", "start"]], "gpsea.model.genome.Strand": [[16, 3, 1, "", "NEGATIVE"], [16, 3, 1, "", "POSITIVE"], [16, 4, 1, "", "is_negative"], [16, 4, 1, "", "is_positive"], [16, 4, 1, "", "opposite"], [16, 2, 1, "", "symbol"]], "gpsea.model.genome.Stranded": [[16, 2, 1, "", "strand"]], "gpsea.model.genome.Transposable": [[16, 4, 1, "", "to_negative_strand"], [16, 4, 1, "", "to_opposite_strand"], [16, 4, 1, "", "to_positive_strand"], [16, 4, 1, "", "with_strand"]], "gpsea.preprocessing": [[17, 1, 1, "", "CohortCreator"], [17, 1, 1, "", "DefaultImpreciseSvFunctionalAnnotator"], [17, 1, 1, "", "FunctionalAnnotator"], [17, 1, 1, "", "GeneCoordinateService"], [17, 1, 1, "", "ImpreciseSvFunctionalAnnotator"], [17, 1, 1, "", "PatientCreator"], [17, 1, 1, "", "PhenopacketOntologyTermOnsetParser"], [17, 1, 1, "", "PhenopacketPatientCreator"], [17, 1, 1, "", "PhenopacketVariantCoordinateFinder"], [17, 1, 1, "", "PreprocessingValidationResult"], [17, 1, 1, "", "ProtCachingMetadataService"], [17, 1, 1, "", "ProteinAnnotationCache"], [17, 1, 1, "", "ProteinMetadataService"], [17, 1, 1, "", "TranscriptCoordinateService"], [17, 1, 1, "", "UniprotProteinMetadataService"], [17, 1, 1, "", "VVHgvsVariantCoordinateFinder"], [17, 1, 1, "", "VVMultiCoordinateService"], [17, 1, 1, "", "VarCachingFunctionalAnnotator"], [17, 1, 1, "", "VariantAnnotationCache"], [17, 1, 1, "", "VariantCoordinateFinder"], [17, 1, 1, "", "VepFunctionalAnnotator"], [17, 5, 1, "", "configure_caching_cohort_creator"], [17, 5, 1, "", "configure_cohort_creator"], [17, 5, 1, "", "configure_default_protein_metadata_service"], [17, 5, 1, "", "configure_protein_metadata_service"], [17, 5, 1, "", "load_phenopacket_files"], [17, 5, 1, "", "load_phenopacket_folder"], [17, 5, 1, "", "load_phenopackets"]], "gpsea.preprocessing.CohortCreator": [[17, 4, 1, "", "process"]], "gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.FunctionalAnnotator": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.GeneCoordinateService": [[17, 4, 1, "", "fetch_for_gene"]], "gpsea.preprocessing.ImpreciseSvFunctionalAnnotator": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.PatientCreator": [[17, 4, 1, "", "process"]], "gpsea.preprocessing.PhenopacketOntologyTermOnsetParser": [[17, 4, 1, "", "default_parser"], [17, 4, 1, "", "process"]], "gpsea.preprocessing.PhenopacketPatientCreator": [[17, 4, 1, "", "process"]], "gpsea.preprocessing.PhenopacketVariantCoordinateFinder": [[17, 4, 1, "", "find_coordinates"]], "gpsea.preprocessing.PreprocessingValidationResult": [[17, 4, 1, "", "is_ok"], [17, 2, 1, "", "policy"], [17, 4, 1, "", "summarize"]], "gpsea.preprocessing.ProtCachingMetadataService": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.ProteinAnnotationCache": [[17, 4, 1, "", "get_annotations"], [17, 4, 1, "", "store_annotations"]], "gpsea.preprocessing.ProteinMetadataService": [[17, 4, 1, "", "annotate"]], "gpsea.preprocessing.TranscriptCoordinateService": [[17, 4, 1, "", "fetch"]], "gpsea.preprocessing.UniprotProteinMetadataService": [[17, 4, 1, "", "annotate"], [17, 4, 1, "", "parse_uniprot_json"]], "gpsea.preprocessing.VVHgvsVariantCoordinateFinder": [[17, 4, 1, "", "find_coordinates"]], "gpsea.preprocessing.VVMultiCoordinateService": [[17, 4, 1, "", "fetch"], [17, 4, 1, "", "fetch_for_gene"], [17, 4, 1, "", "get_response"], [17, 4, 1, "", "parse_multiple"], [17, 4, 1, "", "parse_response"]], "gpsea.preprocessing.VarCachingFunctionalAnnotator": [[17, 4, 1, "", "annotate"], [17, 4, 1, "", "with_cache_folder"]], "gpsea.preprocessing.VariantAnnotationCache": [[17, 4, 1, "", "get_annotations"], [17, 4, 1, "", "store_annotations"]], "gpsea.preprocessing.VariantCoordinateFinder": [[17, 4, 1, "", "find_coordinates"]], "gpsea.preprocessing.VepFunctionalAnnotator": [[17, 3, 1, "", "NONCODING_EFFECTS"], [17, 4, 1, "", "annotate"], [17, 4, 1, "", "fetch_response"], [17, 4, 1, "", "format_coordinates_for_vep_query"], [17, 4, 1, "", "process_response"]], "gpsea.util": [[18, 5, 1, "", "open_resource"], [18, 5, 1, "", "open_text_io_handle_for_reading"], [18, 5, 1, "", "open_text_io_handle_for_writing"]], "gpsea.view": [[19, 1, 1, "", "CohortVariantViewer"], [19, 1, 1, "", "CohortViewer"], [19, 1, 1, "", "DiseaseViewer"], [19, 1, 1, "", "Formatter"], [19, 1, 1, "", "GpseaReport"], [19, 1, 1, "", "MtcStatsViewer"], [19, 1, 1, "", "ProteinVariantViewer"], [19, 1, 1, "", "ProteinVisualizable"], [19, 1, 1, "", "ProteinVisualizer"], [19, 1, 1, "", "VariantFormatter"], [19, 1, 1, "", "VariantTranscriptVisualizer"], [19, 5, 1, "", "summarize_hpo_analysis"]], "gpsea.view.CohortVariantViewer": [[19, 4, 1, "", "process"]], "gpsea.view.CohortViewer": [[19, 4, 1, "", "process"]], "gpsea.view.DiseaseViewer": [[19, 4, 1, "", "process"]], "gpsea.view.Formatter": [[19, 4, 1, "", "format_as_string"]], "gpsea.view.GpseaReport": [[19, 4, 1, "", "write"]], "gpsea.view.MtcStatsViewer": [[19, 4, 1, "", "process"]], "gpsea.view.ProteinVariantViewer": [[19, 4, 1, "", "process"]], "gpsea.view.ProteinVisualizable": [[19, 2, 1, "", "marker_counts"], [19, 2, 1, "", "protein_feature_ends"], [19, 2, 1, "", "protein_feature_names"], [19, 2, 1, "", "protein_feature_starts"], [19, 2, 1, "", "protein_feature_types"], [19, 2, 1, "", "protein_id"], [19, 2, 1, "", "protein_length"], [19, 2, 1, "", "protein_metadata"], [19, 2, 1, "", "transcript_coordinates"], [19, 2, 1, "", "transcript_id"], [19, 2, 1, "", "variant_effects"], [19, 2, 1, "", "variant_locations"], [19, 2, 1, "", "variant_locations_counted_absolute"]], "gpsea.view.ProteinVisualizer": [[19, 4, 1, "", "draw_fig"], [19, 4, 1, "", "draw_protein_diagram"]], "gpsea.view.VariantFormatter": [[19, 4, 1, "", "format_as_string"]], "gpsea.view.VariantTranscriptVisualizer": [[19, 4, 1, "", "draw_variants"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "property", "Python property"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"], "5": ["py", "function", "Python function"], "6": ["py", "data", "Python data"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:property", "3": "py:attribute", "4": "py:method", "5": "py:function", "6": "py:data"}, "terms": {"": [4, 6, 7, 9, 10, 11, 12, 14, 15, 16, 17, 22, 26, 27, 28, 30, 32, 34, 35, 36, 44, 45], "0": [1, 2, 3, 6, 8, 10, 15, 16, 17, 19, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 37, 40, 44, 45], "000": 6, "0000002": 31, "0000078": 31, "0000079": 31, "0000080": 31, "0000098": 37, "0000118": [2, 31, 35], "0000119": 31, "0000152": 31, "0000159": 37, "0000223": 31, "0000234": 31, "0000252": 37, "0000256": 37, "0000271": 31, "0000290": 37, "0000306": 37, "0000309": 37, "0000316": 37, "0000356": 31, "0000359": 31, "0000370": 31, "0000377": 37, "0000407": 27, "0000464": 31, "0000478": 31, "0000486": 26, "0000496": 31, "0000504": 31, "0000517": 40, "0000539": 31, "0000553": 31, "0000562": 23, "0000591": 31, "0000598": 31, "0000707": [31, 35], "0000759": 31, "0000769": 31, "0000777": 31, "0000811": 37, "0000818": 31, "0000820": 31, "0000828": 31, "0000834": 31, "0000847": 31, "0000864": 31, "0000924": 31, "0000927": 31, "0000929": 31, "0000951": 31, "0000971": 31, "0001060": 15, "0001115": 35, "0001155": 31, "0001166": [1, 3, 7], "0001167": [23, 26], "0001172": 26, "0001194": 31, "0001197": 31, "0001199": [23, 26], "0001249": 37, "0001250": [7, 8, 15], "0001256": 37, "0001263": 37, "0001311": 31, "0001392": 31, "0001437": 31, "0001438": 31, "0001446": 31, "0001454": 31, "0001507": 31, "0001511": 37, "0001518": 37, "0001537": 6, "0001551": 31, "0001560": 31, "0001566": 15, "0001567": 15, "0001574": [15, 31], "0001575": 15, "0001578": 15, "0001580": 15, "0001583": 15, "0001587": 15, "0001589": 15, "0001595": 31, "0001597": 31, "0001608": 31, "0001619": 15, "0001620": 15, "0001621": 15, "0001623": 15, "0001624": 15, "0001626": [15, 31], "0001627": [15, 27, 31, 37], "0001628": 15, "0001629": [23, 26], "0001630": 15, "0001631": [15, 23, 26], "0001632": 15, "0001671": [23, 26], "0001684": 26, "0001732": 31, "0001743": 31, "0001760": 31, "0001782": 15, "0001787": [15, 31], "0001792": 15, "0001818": 15, "0001819": 15, "0001821": 15, "0001822": 15, "0001871": 31, "0001872": 31, "0001877": 31, "0001881": 31, "0001889": 15, "0001891": 15, "0001892": [15, 31], "0001893": 15, "0001894": 15, "0001895": 15, "0001906": 15, "0001907": 15, "0001928": 31, "0001939": 31, "0001965": 31, "0001977": 31, "0001999": 37, "0002012": [15, 31], "0002019": 15, "0002086": 31, "0002169": 15, "0002170": 15, "0002187": 37, "0002270": 31, "0002339": 35, "0002342": 37, "00024192670136836828": 26, "000242": 26, "0002585": 31, "0002597": 31, "0002664": 31, "0002715": 31, "0002733": 31, "0002793": 31, "0002795": 31, "0002813": 31, "0002814": 31, "0002817": 31, "0002916": 31, "0002926": 31, "0002973": 31, "0002981": 31, "0002984": [23, 26], "0003011": 31, "0003110": 31, "0003111": 31, "0003117": 31, "0003220": 31, "0003254": 31, "0003256": 31, "0003498": 37, "0003549": 31, "0003621": 17, "0003774": 28, "0003839": 31, "0003974": 26, "0004298": 31, "0004312": 31, "0004322": 37, "0004323": 31, "0004328": 31, "0004329": 31, "0004332": 31, "0004337": 31, "0004352": 31, "0004353": 31, "0004356": 31, "0004360": 31, "0004361": 31, "0004370": 31, "0004371": 31, "0004378": 31, "0004404": 31, "0004408": 31, "0004930": 31, "0005120": [23, 26], "0005368": 31, "0005561": 31, "0005922": [23, 26, 37], "0005927": 26, "0006265": 26, "0006476": 31, "0006490": 31, "0006496": [23, 26], "0006500": 31, "0006529": 31, "0006707": 31, "0006889": 37, "0007686": 31, "0008047": 31, "000899": 23, "0008990549794102921": 23, "0009115": [23, 26], "0009124": 31, "0009127": 31, "0009777": [23, 26], "0009778": 26, "0009809": 31, "0009810": 31, "0009815": [23, 26], "0010696": 35, "0010864": 37, "0010876": 31, "0010881": 31, "0010932": 31, "0010935": 31, "0010936": 31, "0010938": 37, "0010948": 31, "0010968": 31, "0010969": 31, "0010974": 31, "0010977": 31, "0010978": 31, "0010987": 31, "0010991": 31, "0011014": 31, "0011017": 31, "0011018": 31, "0011019": 31, "0011024": 31, "0011025": 31, "0011028": 31, "0011032": 31, "0011043": 31, "0011111": 31, "0011121": 31, "0011122": 31, "0011138": 31, "0011277": 31, "0011297": [23, 26], "0011314": 26, "0011342": 37, "0011343": 37, "0011344": 37, "0011409": 31, "0011442": 31, "0011446": 31, "0011620": 31, "0011623": 26, "0011730": 31, "0011732": 31, "0011733": 31, "0011766": 31, "0011767": 31, "0011772": 31, "0011804": 31, "0011805": 31, "0011842": 31, "0011843": 31, "0011844": [23, 26], "0011869": 31, "0011875": 31, "0011884": 31, "0011893": 31, "0011902": 31, "0011994": [23, 26], "0012029": 31, "0012093": 31, "0012099": 31, "0012103": 31, "0012111": 31, "0012129": 31, "0012130": 31, "0012131": 31, "0012135": 31, "0012143": 31, "0012145": 31, "0012210": 27, "0012243": 31, "0012252": 31, "0012261": 31, "0012285": 31, "0012337": 31, "0012338": 31, "0012345": 31, "0012372": [27, 31], "0012373": 31, "0012379": 31, "0012415": 31, "0012443": [8, 27], "0012447": 31, "0012503": 31, "0012535": 31, "0012591": 31, "0012614": 31, "0012632": 31, "0012638": 31, "0012639": 31, "0012640": 31, "0012647": 31, "0012654": 31, "0012680": 31, "0012681": 31, "0012688": 31, "0012700": 31, "0012718": 31, "0012757": 31, "0012769": 31, "0012772": 31, "0020047": 31, "0020054": 31, "0020058": 31, "0020061": 31, "0020155": 31, "0020169": 31, "0025015": 31, "0025021": 31, "0025031": 31, "0025032": 31, "0025033": 31, "0025065": 31, "0025142": 31, "0025155": 31, "0025276": 31, "0025354": 31, "0025427": 31, "0025429": 31, "0025443": 31, "0025454": 31, "0025456": 31, "0025461": 31, "0025463": 31, "0025546": 31, "0025590": 31, "0025640": 31, "0025668": 31, "0025669": 31, "0025688": 31, "0030085": 31, "0030163": 31, "0030272": 31, "0030338": 31, "0030352": 31, "0030453": 31, "0030680": 31, "0030684": 31, "0030687": 31, "0030800": 31, "0030829": 31, "0030860": 31, "0030872": 31, "0030875": 31, "0030878": 31, "0030956": 31, "0030972": 31, "0031071": 31, "0031072": 31, "0031073": 31, "0031093": 31, "0031094": 31, "0031097": 31, "0031099": 31, "0031101": 31, "0031285": 31, "0031331": 31, "0031340": 31, "0031377": 31, "0031383": 31, "0031389": 31, "0031409": 31, "0031411": 31, "0031416": 31, "0031427": 31, "0031476": 31, "0031508": 31, "0031550": 31, "0031602": 31, "0031653": 31, "0031657": 31, "0031685": 31, "0031703": 31, "0031704": 31, "0031818": 31, "0031850": 31, "0031871": 31, "0031884": 31, "0031910": 31, "0031982": 35, "0032120": 31, "0032180": 31, "0032226": 31, "0032243": 31, "0032245": 31, "0032251": 31, "0032314": 31, "0032367": 31, "0032481": 31, "0032485": 31, "0032488": 31, "0032943": 31, "0033012": 31, "0033013": 31, "0033072": 31, "0033127": 31, "0033170": 31, "0033334": 31, "0033335": 31, "0033354": 31, "0033358": 31, "0033796": 31, "0033799": 31, "0034190": 31, "0034200": 31, "0034251": 31, "0034263": 31, "0034370": 31, "0034430": 31, "0034442": 31, "0034482": 31, "0034552": 31, "0034644": 31, "0034684": 31, "0034698": 31, "0034737": 31, "0034858": 31, "0034899": 31, "0034915": 31, "0034916": 31, "0034977": 31, "0037136715160199273": 26, "0040064": 31, "0040068": 31, "0040069": 31, "0040070": 31, "0040084": 31, "0040085": 31, "0040127": 31, "0040172": 31, "0040203": 31, "0040207": 31, "0040214": 31, "0040224": 31, "0040231": 31, "0045026": 31, "0045027": 31, "0045060": [23, 26], "0045081": 31, "005628510156750059": 23, "005806": 26, "005806240832840839": 26, "01": [23, 26, 27, 28, 30, 34, 35, 37, 40], "0100016": 31, "0100022": 31, "0100491": 31, "0100508": 31, "0100530": 31, "0100536": 31, "0100685": 31, "0100705": 31, "0100763": 31, "0100765": 31, "0100766": 31, "0100767": 31, "0100886": 31, "0100887": 31, "012074957610483744": 27, "02560162393963452": 23, "0410008": 31, "0410009": 31, "0410014": 31, "0430071": 31, "04456405819223913": 26, "04502808125400047": 23, "05": [1, 3, 23, 26, 35], "0500012": 31, "0500015": 31, "0500016": 31, "0500017": 31, "0500018": 31, "0500019": 31, "0500020": 31, "0500114": 31, "0500117": 31, "0500166": 31, "0500183": 31, "0500238": 31, "06": [26, 27], "06200425830044376": 28, "06544319142266644": 26, "06932119159387057": 26, "07": [23, 26, 27, 28, 30, 34, 35, 37, 40], "08470708701170182": 26, "0f": 28, "1": [1, 2, 3, 6, 10, 15, 16, 17, 23, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 40, 44, 45], "10": [2, 6, 8, 15, 17, 19, 23, 25, 26, 27, 28, 30, 35, 37], "100": [2, 23, 26, 35], "1000": 15, "1000029": [6, 15, 45], "1001": [15, 32], "1003": 32, "100del": 23, "100dup": [23, 30], "101": 15, "1024del": 23, "106_107insc": [23, 30], "11": [15, 16, 23, 25, 30, 35], "113": 30, "12": [23, 25, 34], "120": [15, 27, 28, 34], "1221c": [23, 34], "123": [8, 10], "129600": 38, "12_114355723_114355723_g_a": 23, "12_114355755_114355756_tg_t": 23, "12_114355784_114355785_ca_c": 23, "12_114356064_114356065_ta_t": 23, "12_114366207_114366208_gc_g": 23, "12_114366241_114366242_ct_c": 23, "12_114366267_114366267_c_a": 23, "12_114366274_114366274_g_t": 23, "12_114366312_114366312_g_a": 23, "12_114366348_114366349_ct_c": 23, "12_114366360_114366360_c_t": 23, "12_114366366_114366366_t_a": 23, "12_114385474_114385474_a_g": 23, "12_114385475_114385475_c_t": 23, "12_114385521_114385521_c_g": 23, "12_114385521_114385521_c_t": [23, 30], "12_114385522_114385522_g_a": [23, 30], "12_114385550_114385550_a_aattattctcag": 23, "12_114385553_114385553_c_a": 23, "12_114385563_114385563_g_a": [23, 30], "12_114394743_114394746_tgtg_t": 23, "12_114394762_114394763_ca_c": 23, "12_114394817_114394817_g_c": 23, "12_114394820_114394820_c_g": 23, "12_114398568_114398568_c_a": 23, "12_114398578_114398579_ca_c": 23, "12_114398602_114398602_t_g": 23, "12_114398626_114398627_cg_c": 23, "12_114398632_114398632_g_a": 23, "12_114398656_114398656_c_cg": [23, 30], "12_114398666_114398667_tg_t": 23, "12_114398675_114398675_g_t": [23, 30], "12_114398682_114398682_c_cg": [23, 30], "12_114398708_114398709_gc_g": 23, "12_114399514_114399514_a_c": [23, 30], "12_114399559_114399559_t_c": 23, "12_114399594_114399594_a_c": 23, "12_114399613_114399613_t_a": 23, "12_114399622_114399622_g_t": 23, "12_114399625_114399629_acatc_a": 23, "12_114399633_114399633_c_g": 23, "12_114401827_114401827_t_a": 23, "12_114401830_114401830_c_t": [23, 30], "12_114401846_114401846_c_g": 23, "12_114401853_114401853_g_t": 23, "12_114401873_114401874_ta_t": 23, "12_114401907_114401907_a_g": 23, "12_114401921_114401921_c_g": 23, "12_114403754_114403754_g_t": 23, "12_114403792_114403792_c_cg": [23, 30], "12_114403798_114403798_g_gc": [23, 30], "12_114403798_114403799_gc_g": 23, "12_114403859_114403859_g_t": 23, "13": [1, 2, 3, 23, 25, 26, 30], "1304del": 23, "1333del": 23, "13654199434471745": 23, "1366c": 23, "14": [23, 25, 26, 30], "142900": 23, "1435th": 45, "145c": 23, "148": 23, "15": [16, 23, 30], "154700": 38, "1554": 34, "156": [23, 26, 30, 34, 40], "16": 23, "161t": 23, "16436": 28, "16th": 17, "17": [23, 26], "18": [23, 26, 34, 40], "1824c": 15, "18262": 28, "18869165": 34, "18869682": 34, "18921399": 34, "19": [23, 26, 27, 30, 34, 45], "194del": 23, "19723": 28, "1_8358231_8358231_t_c": 45, "1d": 19, "1g": 23, "1st": [6, 15, 34], "2": [2, 3, 4, 6, 9, 10, 12, 15, 16, 17, 23, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 44, 45], "20": [2, 6, 15, 23, 25, 26, 27, 28, 30, 35, 45], "2011": 37, "2015": 21, "2018": [27, 34], "2019": 25, "2022": [29, 37], "2024": 27, "205": 15, "206": 15, "207": 28, "21": 26, "211": 23, "215c": 23, "22": [2, 23, 26, 30], "22280": 28, "222g": 23, "223": 15, "224": 15, "22_10001_20000_inv": [6, 15], "23": [23, 26, 31], "238g": [23, 30], "24": 26, "241a": 23, "243": 23, "246_249del": 23, "25": [15, 26, 28], "250": 34, "251": 30, "253a": 17, "253c": 23, "256000": [7, 8], "25_grch37": 18, "262a": 23, "263": 34, "27": [23, 26, 30], "27bp": 15, "28": [23, 26], "281t": 23, "287": 26, "2986": [8, 15, 25], "299": 34, "29th": 17, "2d": 2, "2nd": 6, "2t": 23, "2x2": 4, "2x3": 4, "3": [2, 4, 15, 17, 23, 27, 28, 31, 32, 35, 36], "30": [15, 17, 23, 26, 30], "3000013": 31, "3000036": 31, "3000050": 31, "303": 25, "30552424": 23, "31": [23, 26], "316a": 23, "32": [23, 26, 30], "320": 34, "321681": 15, "321682": 15, "321887": 15, "33": [23, 26], "34": [23, 26], "346": 34, "348081479150901e": 27, "348081479150902e": 27, "353": 23, "356": [30, 34], "36": [23, 26, 30, 35], "3603": [15, 17], "361t": [23, 30], "36303223": 29, "365": 15, "3652": 15, "369": [23, 26, 40], "374del": 23, "38": [23, 30], "38336121": 23, "4": [2, 6, 8, 10, 15, 17, 23, 26, 27, 28, 30, 34, 35], "40": [2, 23, 30, 35], "4000056": 31, "4000183": 31, "400dup": [23, 30], "4065940176561687": 26, "408c": [23, 30], "40c": 23, "41": [23, 26, 30], "416del": 23, "42": [19, 23, 26], "426dup": [23, 30], "43": [23, 26], "4304a": 45, "432292015291845e": 26, "4375": 15, "44": [23, 26], "45": [23, 26], "450": 35, "451c": 23, "456": 10, "456del": 23, "46": [23, 30, 34], "48": [23, 26], "481a": 23, "4870099714553749": 26, "5": [1, 3, 6, 15, 17, 23, 26, 27, 28, 30, 34, 37, 44, 45], "50": [6, 15, 23, 26, 30, 45], "504del": 23, "50bp": 6, "510": 23, "518": [30, 34], "52": 23, "53": [23, 26, 30], "54": [23, 30], "55": [23, 26], "56": [23, 30], "578": 15, "58": 26, "584g": 23, "587c": 23, "59": 26, "5g": 23, "5th": [6, 15, 23], "5x": 27, "6": [15, 23, 26, 27, 28, 29, 30, 32, 35, 45], "60": 23, "6000062": 31, "6000231": 31, "6000489": 31, "6000673": 31, "614": 25, "6190936213143254e": 23, "62": 23, "63": 26, "630": 25, "64": [23, 26, 35], "641del": 23, "65": 26, "658_660del": 23, "664": 25, "668c": [23, 30], "67": 26, "678g": 23, "680_681insctgagaataat": 23, "69": [25, 26], "7": [1, 3, 6, 10, 15, 23, 30, 35], "709c": [23, 30], "71": [23, 26], "710g": [23, 30], "72": 23, "741216622359659": 25, "75": 26, "755": 23, "7703831604944444": 26, "7735491022101784": 23, "78": 26, "781a": 23, "787g": 23, "798del": 23, "8": [8, 15, 17, 18, 23, 25, 26, 30, 34, 35], "80": [26, 34], "833333333333336": 26, "835c": 23, "84": 26, "85": [23, 30], "873c": 23, "880g": 23, "89": 26, "9": [23, 25, 26, 34], "90": [23, 30, 35], "905del": 23, "93": 26, "939del": 23, "94": 23, "95": [23, 35], "97": 26, "9876g": 15, "99": [26, 35], "A": [2, 3, 6, 7, 8, 10, 12, 15, 17, 19, 21, 23, 30, 32, 34, 35, 37, 39, 41, 44], "AND": [6, 27, 45], "AT": 32, "As": [5, 7, 27, 30, 41, 45], "But": 30, "By": [2, 19, 23, 35, 40], "For": [2, 4, 7, 8, 14, 15, 16, 23, 25, 26, 27, 28, 29, 30, 32, 34, 35, 36, 40, 44, 45], "INS": 15, "If": [2, 3, 6, 11, 13, 15, 17, 18, 23, 26, 35, 37], "In": [2, 4, 8, 15, 17, 21, 23, 26, 27, 28, 29, 30, 33, 34, 35, 37, 40, 41, 44], "It": [1, 3, 4, 23, 30, 35, 43], "NO": 7, "NOT": [2, 15, 16, 25, 45], "No": [1, 3, 16, 23, 30, 34, 40], "Not": 15, "OR": [6, 25, 27, 44, 45], "On": [3, 7, 34], "One": [28, 37, 45], "That": 22, "The": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 43, 44, 45], "Then": [15, 22, 23, 34], "There": [15, 23, 24], "These": [6, 15], "To": [17, 22, 23, 26, 27, 34, 35, 45], "_": [27, 28, 34, 40], "__eq__": 6, "__hash__": 6, "__init__": [15, 17], "__repr__": 6, "__str__": 6, "_api": [2, 3], "_cohort": 15, "_io": 17, "_measur": 25, "_missing_implies_phenotype_exclud": 7, "_stat": 3, "_t": 15, "_tempor": 15, "_term_id": 2, "_variant": 44, "a_label": [6, 23, 25, 26, 27, 28, 44], "a_pred": [6, 23, 25, 26, 27, 28, 44], "aa": 6, "aat": 32, "ab": 6, "abbrevi": [19, 35], "abdomen": 31, "abdomin": 31, "abil": 30, "abnorm": [8, 21, 23, 26, 27, 30, 31, 32, 40], "about": [2, 6, 11, 15, 17, 19, 22, 23, 30, 33, 34, 35, 37, 39, 40], "abov": [6, 22, 31, 34, 37, 38], "absenc": [1, 3, 7, 23, 30, 40], "absens": 30, "absent": [23, 26, 30], "absolut": 6, "abstract": [2, 4, 5, 6, 7, 8, 9, 10, 12, 15, 16, 17, 19], "ac": [36, 44], "ac_": 44, "accept": [15, 17], "acceptor": 23, "access": [6, 15, 16, 17, 22, 23, 27, 34, 35, 40], "accommod": 31, "accord": [2, 3, 23, 26, 31], "account": 35, "acetylaspart": 31, "acid": [15, 30, 31, 34], "across": [2, 19, 33, 43], "actg": 32, "activ": [30, 31], "actual": [30, 34], "ad": 37, "adapt": [8, 31, 37], "add": [22, 39], "addit": [4, 22, 23], "addition": 23, "address": 3, "adenosin": 31, "adiponectin": 31, "adipos": 31, "adjac": 16, "adjust": [26, 37], "adnexa": 31, "adren": 31, "adrenocorticotropin": 31, "advanc": 2, "advantag": [23, 26, 35, 40], "affect": [6, 15, 23, 29, 32, 34, 36, 45], "affected_exon": 15, "affects_egfr": 36, "affects_lmna": 36, "after": [1, 3, 17, 22], "ag": [0, 10, 11, 15, 17, 23, 28, 30, 37], "against": 29, "age_of_death": 15, "aii": 28, "aiii": 28, "al": [8, 21, 25, 27, 29, 34, 37], "ala143argfster40": [23, 30], "ala34glyfster27": [23, 30], "ala34profster32": [23, 30], "albumin": 31, "aldosteron": 31, "alel": 44, "align": 15, "aliv": [11, 15], "all": [1, 2, 3, 5, 6, 7, 8, 15, 17, 22, 26, 28, 31, 32, 33, 34, 39, 41, 42, 44, 45], "all_count": [1, 3], "all_diseas": 15, "all_measur": 15, "all_pati": 15, "all_phenotyp": 15, "all_transcript_id": 15, "all_vari": 15, "all_variant_info": 15, "allel": [6, 7, 8, 15, 21, 26, 27, 28, 29, 33, 39, 44, 45], "allele_count": [5, 6, 36], "allelecount": [5, 6], "allianc": 21, "allow": [3, 30, 33, 34, 35, 41, 44], "allow_nan": 14, "alon": 35, "along": [14, 26, 34, 36, 39], "alpha": [1, 3, 26, 31, 35], "alreadi": 34, "also": [15, 31, 34, 39, 40], "alt": [15, 32], "altern": [6, 12, 15, 27, 30, 32, 35, 36], "although": 30, "alwai": [6, 15, 16, 34], "amaz": 34, "amino": [15, 30, 31], "aminoacid": [6, 15, 16, 19, 34], "amniot": 31, "among": [2, 15], "amount": [8, 34], "amyloid": 31, "an": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 44, 45], "analys": [1, 33, 34, 41, 44], "analysi": [0, 15, 17, 19, 21, 24, 29, 33, 34, 36, 37, 38, 40, 41, 43, 44, 45], "analysisresult": [0, 1, 3], "analyz": [0, 8, 10, 19, 23, 25, 27, 28, 30, 41], "anatomi": [23, 34], "ancestor": [7, 23, 32, 40], "andolfo": 34, "aneurysm": 32, "angiotensin": 31, "ani": [2, 5, 6, 8, 14, 15, 17, 26, 27, 30, 34, 35, 36, 37, 38, 45], "ank": [6, 15], "ankyrin": 15, "annot": [2, 6, 7, 11, 15, 17, 19, 23, 26, 30, 32, 34, 35, 40, 45], "annotation_frequency_threshold": [2, 35], "anomali": [27, 37], "anoth": [7, 16, 23, 34], "answer": 6, "anterior": [31, 40], "antimullerian": 31, "anu": 31, "api": [15, 17, 21, 26, 30, 41, 45], "aplasia": [23, 26], "apoptosi": 31, "appear": 31, "appendicular": [23, 26], "appli": [1, 3, 9, 32, 35], "applic": 23, "apply_predicates_on_pati": [1, 3], "approach": [33, 35], "appropri": [23, 24, 30], "ar": [1, 2, 3, 6, 8, 9, 10, 15, 16, 17, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 37, 40, 41, 44, 45], "arachnodactyli": 7, "arbitrari": [14, 16], "areolar": 31, "arg": 14, "arg134profster49": [23, 30], "arg237gln": [23, 30], "arg237pro": 23, "arg237trp": [23, 30], "arg279ter": [23, 30], "arg81trp": 23, "arginin": 45, "argument": [8, 13, 18, 19, 35, 36, 40], "arithmet": 16, "arm": 31, "aromatas": 31, "around": [4, 9, 12, 15], "arrai": [4, 19], "arrang": 31, "arrhythmia": 23, "arriv": 35, "ask": [2, 21], "aspect": [19, 30], "assai": [23, 30], "assembl": 17, "assembli": 16, "assert": [15, 16], "assess": [1, 3, 15, 27, 37], "assign": [1, 3, 5, 6, 7, 8, 10, 15, 26, 27, 37, 38, 39, 41, 44, 45], "assist": 33, "associ": [1, 3, 8, 15, 17, 21, 23, 25, 29, 30, 34, 41], "assum": [15, 16, 17, 25, 35], "assumpt": [35, 40], "atrial": [23, 26, 30, 31], "atrium": [23, 26], "atrophi": 27, "atrophin": 27, "attach": 15, "attain": [1, 3, 28], "attribut": [3, 6, 7, 15, 21], "automat": 27, "autonom": 31, "autosom": [23, 44], "avail": [1, 2, 10, 15, 17, 21, 23, 26, 27, 30, 34, 41, 45], "avoid": [19, 31], "ax": [8, 10, 19, 23, 27, 28, 30, 34], "axi": [27, 28, 31, 36, 39], "b": [6, 15, 16, 35, 44], "b_label": [6, 23, 25, 26, 27, 28, 44], "b_predic": [6, 23, 25, 27, 28, 44], "back": [13, 17, 34], "background": [21, 33], "backup": 15, "bandwidth": 34, "base": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 23, 26, 27, 31, 32, 34, 36, 37, 38, 41, 43], "baseview": 19, "basi": 30, "basic": [15, 16, 34, 45], "batteri": 7, "bb": 6, "becaus": [2, 15, 29, 30, 31, 32, 35, 37], "been": [10, 15, 23, 26, 34, 35], "befor": [15, 45], "behavior": 21, "behind": [23, 40], "being": [1, 2, 3, 12, 16, 17, 19, 23, 30, 35, 37, 41, 45], "belong": [2, 15], "below": [6, 32], "benjamini": [1, 3, 23, 26, 35], "besid": 34, "best": 21, "beta": [31, 34], "better": 45, "between": [3, 8, 10, 11, 15, 16, 19, 21, 23, 25, 26, 27, 28, 30, 32, 35, 37, 43], "beyond": 6, "bia": [15, 34], "biallel": 6, "biallelic_pred": [5, 6, 25, 44], "big": 25, "bin": [1, 3, 5, 6, 23, 27, 35], "bind": 15, "biolog": [15, 16, 27, 34], "biologi": 21, "biomark": 31, "biomed": [23, 34], "biopterin": 31, "birth": [15, 31], "bit": 40, "bleed": 31, "blood": 31, "bodi": 31, "boiler": 34, "boilerpl": 34, "bone": [23, 26, 31], "bonferroni": [23, 35], "bool": [2, 6, 7, 10, 15, 16, 17, 19], "boolean": 15, "borderlin": 37, "both": [1, 4, 15, 17, 23, 37, 38, 41, 44], "bound": [16, 17], "boundari": [15, 16], "box": [8, 27, 30, 34], "bp": [6, 15, 32, 45], "brain": [8, 27], "branch": [22, 35], "break": 15, "breakend": 15, "breakpoint": [6, 15, 17], "breast": 31, "breath": 31, "brief": 21, "bring": [23, 31], "bronchu": 31, "buccal": 31, "bug": 21, "build": [6, 15, 16, 17, 23, 26], "built": 34, "burden": [2, 3, 23, 35], "c": [5, 15, 17, 21, 23, 25, 27, 30, 32, 34, 45], "c17998": 15, "c46112": 15, "c46113": 15, "cach": [13, 17, 34], "cache_dir": 17, "cache_env": [0, 13], "calcium": 31, "calcul": [4, 8, 9, 12, 15, 16, 26, 30], "calf": 31, "call": [14, 15, 31, 34, 35], "callabl": [8, 18], "can": [2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 22, 23, 26, 27, 28, 30, 31, 34, 35, 36, 37, 38, 39, 40, 44, 45], "cannot": [5, 8, 10, 11, 15, 17, 27, 34, 37, 41], "canon": 15, "cap": 35, "capabl": 41, "carboxyl": 31, "cardiac": [23, 26, 30, 31], "cardiomyocyt": 31, "cardiovascular": 31, "carpal": [23, 30], "carri": [27, 29, 34], "cart": 31, "cascad": 31, "case": [2, 8, 15, 17, 23, 26, 27, 30, 34, 40], "cat_id": [1, 5, 8, 10, 25, 27], "catalyt": 30, "cataract": 35, "catecholamin": 31, "categor": [2, 5, 6, 7, 30, 39, 44], "categori": [1, 3, 5, 7, 8, 10, 15, 25, 26, 27, 33, 34, 36, 37, 39], "catheter": 31, "caudat": 35, "caus": [21, 40], "caviti": 31, "ccc": 32, "cct": 15, "cd": [15, 22], "cdna": [15, 23], "cds_end": 15, "cds_start": 15, "cell": [30, 31], "cellular": 31, "censor": [10, 11], "central": 31, "cerebellar": 27, "certain": [6, 15, 30, 35, 39, 45], "certainli": 34, "cg": 32, "chanc": [23, 26, 35], "chang": [6, 15, 27, 33, 34, 45], "change_length": [6, 15, 27, 45], "charact": 15, "character": [15, 23], "characterist": 15, "check": [1, 3, 4, 6, 15, 16, 17, 23, 35, 45], "check_circular": 14, "checker": 34, "checkout": 22, "child": 2, "children": [31, 35], "chin": 37, "choic": [15, 33], "choos": [6, 17, 23, 26, 30, 33], "chosen": [15, 23, 26, 34], "chr1": [15, 16, 32], "chr5": 15, "chrom": [15, 32], "chromosom": [6, 15, 17, 29, 31, 45], "chromosomal_delet": 45, "chronic": 28, "chrx": 16, "cilium": 31, "circul": 31, "cl": [14, 25, 26, 27, 28, 30, 34, 45], "class": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 19, 23, 30, 34, 35, 45], "classifi": 26, "clearanc": 31, "clearli": 45, "click": [15, 34], "clinic": [15, 23, 25, 34, 35, 37, 40], "clinvar": [23, 34], "clone": 22, "cluster": 39, "cm000663": 16, "coagul": 31, "code": [1, 2, 3, 8, 15, 17, 22, 23, 26, 27, 28, 30, 34], "coding_sequence_vari": 15, "codon": [15, 21, 34, 45], "cohort": [0, 2, 3, 6, 7, 8, 10, 15, 17, 19, 21, 33, 36, 41, 42], "cohort_cr": [17, 23, 34, 40], "cohort_nam": 23, "cohort_s": 2, "cohortcr": [0, 17, 34], "cohortvariantview": [0, 19, 23], "cohortview": [0, 19, 23, 30], "coiled_coil": 15, "collect": [2, 5, 6, 7, 9, 12, 15, 17, 21, 23, 34, 40], "color": 8, "column": [1, 2, 3, 8, 10, 15, 28], "com": 22, "combin": [15, 23, 45], "come": [16, 27, 30], "command": 22, "common": [1, 23, 29, 30], "commonli": [16, 35], "compact": [6, 15], "compar": [4, 9, 10, 11, 12, 15, 24, 28, 29, 33, 38, 43, 44], "compare_genotype_vs_phenotyp": [3, 23, 26], "compare_genotype_vs_phenotype_scor": [8, 25, 27], "compare_genotype_vs_surviv": [10, 28], "comparison": [10, 15, 29, 44], "compil": 15, "complain": 17, "complet": [15, 17, 34, 35, 44], "complete_record": 1, "complex": 35, "compon": [27, 45], "composit": [15, 31, 34], "compositional_bia": 15, "compound": [6, 29, 31, 45], "comprehens": [21, 40], "comput": [1, 3, 6, 8, 9, 10, 11, 12, 17, 23, 26, 27, 28, 44], "compute_pv": [4, 9, 12], "compute_surviv": 10, "concentr": 31, "concept": [21, 32, 35], "conceptu": 15, "concern": [21, 27], "concis": 15, "conclus": 35, "condens": 31, "condit": [27, 35], "conduct": [23, 26, 30], "config": 0, "configur": [3, 6, 17, 23], "configure_caching_cohort_cr": [0, 17, 23, 34, 40], "configure_cohort_cr": [0, 17], "configure_default_protein_metadata_servic": [0, 17, 30, 34], "configure_hpo_term_analysi": [1, 3, 23, 26], "configure_ontology_stor": [23, 26, 27, 28, 30, 34, 35, 37, 40], "configure_phenopacket_registri": [23, 34, 40], "configure_protein_metadata_servic": [0, 17, 23], "congenit": [23, 26, 27], "connect": 31, "consequ": 15, "conserv": 15, "consid": [4, 6, 15, 16, 17, 26, 27, 31, 37], "consider": 31, "consist": [2, 15, 16, 34, 35], "consortium": 27, "constitut": 31, "construct": [17, 27, 40], "constructor": [2, 15, 35], "consult": [13, 30], "contain": [1, 2, 8, 15, 16, 17, 19, 23, 28, 31, 34], "contains_po": 16, "contemporari": 30, "content": 34, "context": [2, 21, 27, 35, 44], "contig": [15, 16, 34], "contig_by_nam": [15, 16, 32], "contigu": 16, "conting": [2, 3, 4, 26], "contingency_t": 26, "continuouspartit": [8, 10], "contrast": 37, "contribut": 30, "control": [23, 35], "conveni": [7, 17, 26, 34], "convers": 32, "convert": 17, "coordin": [6, 15, 16, 17, 19, 30, 32], "copi": 29, "cord": 31, "corneal": 31, "corpuscular": 31, "correct": [1, 3, 23, 26, 31, 33], "corrected_pv": [1, 3], "correctli": 17, "correl": [0, 1, 2, 3, 21, 23, 24, 30, 31, 33, 34, 35, 45], "correspon": 28, "correspond": [1, 2, 3, 6, 7, 8, 15, 16, 17, 23, 26, 27, 30, 32, 33, 35, 37, 44, 45], "cortisol": 31, "could": [1, 3, 14], "count": [1, 2, 3, 4, 6, 7, 8, 15, 19, 23, 26, 27, 30, 31, 33, 34, 37, 39, 44], "count_al": 15, "count_deceas": 15, "count_distinct_diseas": 15, "count_distinct_hpo_term": 15, "count_distinct_measur": 15, "count_femal": 15, "count_mal": 15, "count_statist": [3, 26, 35], "count_unique_diseas": 15, "count_unique_measur": 15, "count_unique_phenotyp": 15, "count_unknown_sex": 15, "count_unknown_vital_statu": 15, "count_with_age_of_last_encount": 15, "count_with_disease_onset": 15, "counter": 15, "countingphenotypescor": [1, 8, 27], "counts_fram": 2, "countstatist": [3, 4], "coveni": 15, "cover": [5, 41], "cpd_viewer": 30, "cranial": 31, "creat": [2, 6, 7, 8, 13, 15, 16, 17, 19, 21, 23, 25, 26, 27, 28, 30, 33, 35, 36, 37, 40, 44, 45], "create_variant_from_scratch": 15, "creator": 17, "criteria": [6, 39, 45], "criterion": 6, "cry": 31, "csf": 31, "ct": 15, "culprit": 2, "curat": 23, "curi": [2, 6, 8, 15, 17], "current": [13, 15, 16, 17, 18, 19, 22, 34, 43], "custom": [8, 34, 44], "cut": 40, "cycl": 31, "cyp21a2": 25, "cystein": 15, "cytologi": 31, "cytometri": 31, "d": 15, "dai": [15, 17, 28], "danger": 30, "darksalmon": 8, "data": [1, 2, 3, 4, 8, 10, 15, 16, 17, 19, 21, 23, 25, 26, 27, 30, 33, 35, 39, 40, 45], "data_column": 1, "databas": 17, "datadir": 17, "datafram": [1, 2, 3, 4, 8, 10, 15, 19, 28, 34], "dataset": [23, 26, 30], "days_in_month": 15, "days_in_week": 15, "days_in_year": [15, 28], "de": [8, 33, 42], "death": [10, 11, 15], "decad": 28, "deceas": [11, 15], "decid": [2, 15, 30, 31], "decilit": 15, "decis": 2, "decod": [14, 18, 34], "deem": 31, "deep": 21, "def": [8, 14], "default": [2, 3, 6, 13, 14, 17, 18, 19, 23, 34, 35, 40, 44], "default_cache_path": [0, 13], "default_filt": [2, 26, 35], "default_pars": 17, "defaultimprecisesvfunctionalannot": [0, 17], "defaulttermid": 2, "defect": [23, 26, 27, 30, 32], "defin": [3, 5, 6, 15, 28, 32, 36, 44], "definit": 15, "degre": 37, "dehydr": 34, "del": [6, 15, 32, 45], "delet": [6, 15, 23, 32, 45], "deliveri": 31, "demonstr": [23, 45], "denot": [15, 21, 37], "depend": [1, 23, 24], "deposit": [26, 27], "deriv": 35, "descend": [6, 7, 8, 23, 27, 32, 37, 40], "describ": [8, 15, 17, 22, 25, 26, 27, 28, 30, 35, 37, 40, 44, 45], "descript": [6, 7, 8, 15, 17, 25, 26, 27, 28, 36, 37, 40, 45], "design": [21, 30, 34, 35], "desir": [6, 17, 29, 31, 41], "despit": 23, "detail": [15, 23, 28, 35], "detect": 30, "determin": [6, 15, 17, 27, 35, 37], "develop": [15, 22, 28, 31, 35, 37], "deviat": [21, 26], "devri": [30, 37], "devriesphenotypescor": [1, 8, 27, 37], "df": [15, 34], "diagnos": [6, 7, 11, 15, 23, 30, 38, 39], "diagnosi": [6, 7, 11, 15, 33, 39], "diagnosis_pred": [5, 6, 38], "diagram": [19, 23, 30, 34], "dialog": 34, "dichotom": 26, "dict": [14, 17], "differ": [8, 10, 15, 16, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 41, 43, 44], "differenti": 21, "digest": 31, "digit": [23, 26], "dimension": 15, "dingeman": 37, "diploid": 15, "direct": [7, 15, 23, 35], "directori": [13, 17, 34], "disabl": [27, 35, 37], "discharg": 31, "discoveri": [23, 35], "discret": [3, 4, 5, 41], "diseas": [0, 6, 7, 11, 15, 21, 23, 28, 30, 36, 38, 39, 40, 44], "disease_by_id": 15, "disease_id": 11, "disease_id_queri": 7, "disease_onset": [10, 11], "diseaseanalysi": [1, 3], "diseasepresencepred": [5, 7], "diseaseview": [0, 19], "disord": [23, 30, 34], "displai": [2, 6, 19, 23, 30, 34], "disproportion": 37, "distanc": 16, "distance_to": 16, "distinct": [15, 23, 30], "distribut": [8, 12, 15, 19, 27, 33, 43], "divid": [26, 39], "dl": 15, "dna": [16, 31], "do": [2, 6, 8, 16, 17, 19, 22, 23, 26, 34, 35, 40, 45], "doc": [25, 26, 27, 28, 30, 34, 45], "document": [21, 22, 24, 30, 34, 35], "doe": [2, 11, 13, 15, 17, 32], "domain": [2, 6, 15, 27, 31, 33, 34, 35, 45], "domin": [23, 29, 44], "done": [16, 22, 36, 39, 45], "donor": [15, 23], "dopamin": 31, "doubl": [8, 16], "down": [17, 40], "download": [15, 34], "downloaded_uniprot_json": 34, "downstream": [2, 16, 34, 41], "downstream_gene_vari": [15, 17], "dpi": [27, 28, 34], "dr": 26, "draw": [8, 10, 19, 34], "draw_fig": [19, 34], "draw_protein_diagram": [19, 23, 30], "draw_vari": 19, "drawn": 19, "driven": 31, "drop": 28, "drug": 31, "due": [15, 17], "dump": 14, "dup": 15, "duplic": [15, 17, 32], "durat": 15, "dure": 15, "e": [1, 2, 3, 6, 7, 8, 10, 11, 15, 16, 17, 18, 21, 23, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 40, 44], "each": [1, 2, 3, 6, 7, 8, 10, 15, 17, 19, 21, 23, 26, 27, 28, 29, 30, 33, 35, 37, 41], "ear": 31, "easi": [22, 43], "easiest": 34, "easili": [19, 38], "ectopia": [38, 40], "eff": [27, 45], "effect": [6, 15, 17, 23, 27, 30, 34, 44, 45], "either": [2, 6, 7, 8, 15, 16, 19, 26, 27, 34, 37], "elabor": 45, "electrolyt": 31, "electrophysiologi": 31, "element": [15, 16, 17, 19], "els": 14, "elsewher": [28, 30], "embryon": 31, "empir": 28, "empti": [15, 16, 17], "enabl": 22, "encod": [6, 7, 14, 15, 17, 18, 23, 25, 26, 27, 28, 34, 45], "encount": [11, 15, 23, 30], "end": [6, 15, 16, 17, 23, 28, 32, 34], "end_on_strand": 16, "endocrin": 31, "endpoint": [1, 10], "energi": 31, "enrich": 35, "ensembl": 15, "enst00000123456": 15, "ensur": [18, 44], "ensure_ascii": 14, "enter": 30, "entir": 34, "entiti": [7, 15, 16, 17], "entri": [17, 34, 40], "enum": [15, 16], "enumer": 19, "environ": [13, 19, 22, 30], "enzym": 31, "epiphysi": 31, "equal": [1, 3, 6, 15, 27, 35], "equival": [8, 27], "error": [15, 17, 23, 30, 34, 35], "erythrocyt": 31, "erythroid": 31, "erythropoietin": 31, "et": [8, 21, 25, 27, 29, 34, 37], "etc": [15, 17], "evalu": [6, 21, 26, 27], "even": [3, 31, 34, 35], "ever": 2, "everi": 28, "exact": [1, 3, 4, 6, 8, 15, 17, 21, 23, 24, 27, 29, 30, 33, 35], "exactli": [6, 8, 35], "exampl": [1, 3, 4, 6, 7, 8, 9, 10, 14, 15, 17, 19, 23, 24, 29, 32, 33, 35, 38, 41, 45], "except": [14, 17, 45], "exclud": [2, 5, 7, 15, 16, 23, 26, 36, 40], "excluded_diseas": 15, "excluded_member_count": 15, "excluded_phenotyp": 15, "exclus": [5, 7, 23, 32, 41], "execut": [10, 25, 27, 28], "exemplifi": 30, "exercis": [31, 34], "exhaust": 5, "exibit": 7, "exist": [13, 17, 30, 35], "exon": [6, 15, 23, 28, 34, 45], "exon20": 45, "exon_numb": 6, "exons_effect": 15, "expect": [2, 15, 17, 18, 26, 27, 31, 34, 35, 39], "expenditur": 31, "experiment": 30, "explan": [2, 24, 42], "explicit": [2, 7, 35], "explicitli": [15, 40], "explor": [26, 27, 33, 34, 40], "exploratori": 33, "expos": 26, "express": [10, 17, 26, 31], "extend": 27, "extern": 37, "extract": [15, 17], "extraocular": 31, "extrem": [23, 26, 35], "ey": [27, 31, 40], "f": [8, 21, 28], "face": 31, "fact": [35, 45], "factor": [30, 31, 34, 35, 39], "factori": 2, "fail": [2, 15], "fall": [8, 13], "fallback": [13, 17], "fals": [2, 3, 6, 7, 10, 14, 15, 16, 17, 23, 26, 28, 30, 35], "famili": [15, 23, 35, 38], "far": 27, "farthest": 27, "fascia": 31, "fbn1": [6, 15], "fdr": [26, 35], "fdr_bh": [1, 3, 23, 26, 35], "fdr_by": 35, "fdr_gb": 35, "fdr_tsbh": 35, "fdr_tsbky": 35, "featur": [6, 7, 10, 15, 21, 22, 26, 27, 30, 40, 45], "feature_elong": 15, "feature_id": 6, "feature_trunc": 15, "feature_typ": [6, 15], "featureinfo": [0, 15], "features": 30, "featuretyp": [0, 6, 15], "fecal": 31, "feel": 41, "feenstra": [8, 37], "femal": [15, 23, 30, 43], "fet": [24, 30, 33], "fetal": 31, "fetch": [17, 23, 30, 33], "fetch_for_gen": 17, "fetch_respons": 17, "few": [32, 34, 45], "fh": [18, 19, 25, 26, 27, 28, 30, 45], "fiber": 31, "fibrillin": 15, "fibrinolysi": 31, "fibroblast": 31, "fiction": [6, 44], "field": [11, 15, 29], "fig": [23, 27, 28, 30, 34], "figsiz": [23, 27, 28, 30, 34], "figur": [17, 19, 34], "file": [15, 17, 18, 19, 25, 26, 27, 28, 30, 34, 45], "filter": [2, 3, 15, 23, 26, 31, 32, 33], "filter_method_nam": 2, "final": [26, 40], "find": [3, 16, 17, 23, 26, 34, 35, 39], "find_coordin": 17, "finder": 17, "finger": [15, 23, 26], "fingertip": 34, "finish": 25, "finit": 10, "first": [6, 13, 15, 23, 26, 27, 30, 34, 35, 36, 39], "fisher": [1, 3, 4, 21, 23, 24, 29, 30, 33, 35, 42], "fisher_exact": [4, 26], "fisherexacttest": [3, 4, 26, 35], "fit": 15, "five": 27, "five_prime_utr_vari": [15, 17], "fix": [34, 36], "flexibl": [26, 45], "flip": 16, "float": [1, 2, 3, 8, 9, 10, 15, 17, 26, 27], "flow": 31, "fluid": 31, "focal": 32, "focu": [21, 23], "fold": 15, "folder": [13, 17, 34], "follow": [3, 6, 10, 11, 15, 22, 23, 25, 26, 27, 28, 30, 31, 32, 34, 35, 37, 41, 44, 45], "foot": 31, "for_sampl": 15, "forearm": 31, "forehead": 37, "form": [4, 31, 34], "formal": 30, "format": [7, 15, 16, 17, 19, 30, 34], "format_as_str": 19, "format_coordinates_for_vep_queri": 17, "formatt": [0, 19], "formul": [30, 34], "forward": 16, "found": [15, 17, 23, 27, 30, 34, 35, 37], "four": [30, 34], "fpath_cache_dir": 17, "fpath_cohort": 30, "fpath_cohort_json": [25, 26, 27, 28, 45], "fragment": 15, "frame": [1, 2, 3, 4, 8, 10, 15, 19, 25, 27, 34, 45], "frameshift": [44, 45], "frameshift_vari": [15, 23, 26, 27, 30, 44, 45], "framework": 27, "free": 41, "frequenc": [2, 19, 23, 26, 35], "frequent": [23, 30, 32], "friendli": 2, "from": [2, 5, 6, 8, 10, 11, 12, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32, 33, 35, 36, 37, 38, 40, 41, 43, 44, 45], "from_curi": 40, "from_feature_fram": [15, 34], "from_iso8601_period": 15, "from_map": 15, "from_measurement_id": [8, 25], "from_pati": 15, "from_query_curi": [8, 27], "from_raw_part": 15, "from_str": 15, "from_term": 15, "from_uniprot_json": [15, 34], "from_vcf_liter": [15, 32], "from_vcf_symbol": [15, 32], "fuction": 17, "func": 8, "funcformatt": 28, "function": [4, 6, 7, 8, 9, 12, 15, 17, 18, 23, 26, 27, 30, 31, 34, 40, 44, 45], "functional_annot": 17, "functionalannot": [0, 17], "functionalannotationawar": [0, 15], "further": [23, 27, 40], "furthermor": 34, "fwer": 35, "g": [1, 2, 3, 6, 7, 8, 10, 11, 15, 16, 17, 18, 21, 23, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 40, 44, 45], "ga": 31, "ga4gh": [15, 21, 23, 25, 26, 27, 28, 33, 45], "gain": 23, "galleri": 33, "ganglion": 31, "gastrin": 31, "gastrointestin": 31, "gather": 30, "gb_acc": 16, "gcf_000001405": 18, "ge": [26, 44], "genbank": 16, "genbank_acc": 16, "gene": [6, 15, 17, 23, 26, 27, 29, 30, 34, 36, 40, 45], "gene_coordinate_servic": 17, "gene_id": 15, "gene_nam": 15, "gene_symbol": 15, "genecoordinateservic": [0, 17], "gener": [1, 2, 3, 5, 7, 15, 17, 19, 21, 23, 26, 30, 33, 41], "general_hpo_term": 2, "genet": 21, "genit": 31, "genitalia": 37, "genitourinari": 31, "genom": [6, 15, 17, 18, 21, 23, 30, 32, 34, 45], "genome_build": [17, 23, 30, 34], "genome_build_id": 16, "genomebuild": [15, 16, 17], "genomebuildidentifi": [15, 16], "genomicinterpret": 17, "genomicregion": [15, 16, 34], "genotyp": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 17, 21, 24, 30, 31, 33, 36, 38, 41, 43, 45], "genotype_for_sampl": 15, "genotypepolypred": [1, 2, 3, 5, 6, 8, 10, 41], "gestat": [11, 15, 37], "gestational_dai": 15, "get": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 15, 16, 17, 18, 19, 33, 35], "get_annot": 17, "get_cache_dir_path": [0, 13, 17], "get_categor": [5, 7, 25, 27], "get_categori": 5, "get_category_nam": 5, "get_cds_region": [15, 34], "get_coding_base_count": [15, 34], "get_codon_count": [15, 34], "get_excluded_count": 15, "get_features_variant_overlap": 15, "get_five_prime_utr": [15, 34], "get_hgvs_cdna_by_tx_id": 15, "get_maximum_group_observed_hpo_frequ": 2, "get_number_of_observed_hpo_observ": 2, "get_patient_id": 15, "get_preferred_tx_annot": 15, "get_quest": 6, "get_respons": 17, "get_three_prime_utr": 15, "get_tx_anno_by_tx_id": 15, "get_variant_by_kei": [15, 45], "gg": [15, 17], "git": 22, "github": [22, 41], "give": [6, 34], "given": [2, 6, 7, 10, 15, 17, 18, 19, 37, 40], "gland": 31, "glial": 31, "gln151ter": 23, "gln302argfster92": [23, 30], "gln315argfster79": [23, 30], "gln421ter": 15, "gln456ter": 23, "gln49ly": 23, "global": [21, 37], "globe": [31, 37], "glossari": 33, "glu294ter": [23, 30], "glucagon": 31, "glucocorticoid": 31, "glucos": 31, "gly125alafster25": 23, "gly195ala": 23, "gly80arg": [23, 30], "glycolipid": 31, "glycoprotein": 31, "glycosaminoglycan": 31, "glycosyl": 31, "go": 15, "gonadotropin": 31, "good": [23, 34], "gov": 29, "gp": 23, "gpc": 33, "gpsea": [20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45], "gpsea_cach": [13, 17], "gpsea_cachedir": 13, "gpseajsondecod": [0, 14, 25, 26, 27, 28, 30, 34, 45], "gpseajsonencod": [0, 14, 34], "gpseareport": [0, 19, 30], "granulocytopoiet": 31, "graph": [7, 26], "graphic": [19, 26, 30], "grch37": [16, 17, 34], "grch38": [15, 16, 17, 23, 30, 32, 34], "great": 35, "greater": 35, "grid": [27, 28], "group": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 28, 29, 33, 34, 37, 39, 41, 45], "group1": 27, "group2": 27, "group_label": [5, 23, 25, 26, 27, 28, 36, 38, 40, 43, 44], "growth": [31, 34], "gt": 15, "gt_col": 1, "gt_id_to_nam": [25, 27], "gt_predic": [1, 2, 3, 8, 10, 23, 25, 26, 27, 28, 36, 38, 43, 44], "guid": [21, 23, 34], "h": [15, 35], "h_1": 4, "ha": [1, 2, 3, 6, 7, 8, 10, 11, 15, 16, 23, 26, 27, 30, 31, 34, 37], "had": [2, 23, 30], "hair": 31, "hallmark": 7, "hand": [23, 26, 31, 34, 37], "handl": [5, 18, 19], "happen": 3, "harbor": [27, 36, 44], "has_sv_info": 15, "has_variant_coordin": 15, "hashabl": 15, "have": [2, 8, 15, 26, 34, 35, 37, 44], "head": [25, 27, 28, 31], "health": 21, "hear": 27, "heart": [23, 26, 27, 31, 37], "height": 31, "helic": 15, "help": 23, "hematocrit": 31, "hemizyg": 15, "hemoglobin": 31, "henc": [22, 26], "hepat": 31, "hepatobiliari": 31, "here": [1, 6, 16, 23, 27, 28, 32, 34, 37, 40, 41, 44], "hereditari": 34, "heterozyg": [15, 26, 36, 39], "heterozygot": 29, "heurist": [2, 23, 31, 35], "hgnc": [15, 17], "hgv": [15, 17, 19, 23, 30], "hgvs_cdna": 15, "hgvs_coordinate_find": 17, "hgvsp": 15, "hierarch": 31, "hierarchi": [2, 28, 37, 40], "high": 15, "higher": [26, 27, 37], "highest": 15, "hip": 31, "his1435arg": 45, "his220del": 23, "his445metfster137": 23, "histidin": [15, 45], "histori": 35, "hkd": 30, "hmf01": [23, 26], "hmf02": 2, "hmf03": 2, "hmf05": 2, "hmf07": 2, "hmf08": [2, 23, 26], "hmf09": [23, 26], "ho": 35, "hochberg": [1, 3, 23, 26, 35], "holm": 35, "holt": [23, 30, 45], "homeostasi": 31, "hommel": 35, "homo": 6, "homovanil": 31, "homozygot": 29, "homozygous_altern": 15, "homozygous_refer": 15, "honeydew": 8, "hormon": 31, "how": [16, 22, 23, 24, 34, 40, 45], "howev": [5, 10, 16, 22, 23, 26, 32, 39, 41, 45], "hp": [1, 2, 3, 7, 8, 15, 17, 23, 26, 27, 28, 31, 35, 37, 40], "hpo": [2, 3, 7, 8, 11, 15, 17, 19, 21, 25, 26, 28, 30, 33, 34, 37, 41, 42], "hpo_mtc": 35, "hpo_onset": [10, 11, 28], "hpomtcfilt": [1, 2, 3, 23, 26, 35], "hpopred": [5, 7, 40], "hpotermanalysi": [1, 3, 26, 35, 40], "hpotermanalysisresult": [1, 3, 19], "hpotk": [2, 3, 23, 26, 27, 28, 30, 34, 35, 37, 40], "html": 19, "http": [22, 29], "human": [2, 15, 16, 19, 21, 30, 34, 37], "humor": 31, "hundr": 35, "hypertelor": 37, "hypoplasia": [23, 26, 30], "hypothalamu": 31, "hypothes": [26, 30, 33, 34, 35], "hypothesi": [2, 12, 23, 26, 30, 35], "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 39, 40, 41, 43, 44, 45], "id": [1, 5, 6, 7, 8, 10, 15, 17, 19, 23, 31, 32, 34, 39], "ident": 29, "identifi": [1, 6, 8, 15, 16, 23, 28, 30, 31, 34, 37, 38], "idividu": 26, "idx": 2, "ignor": [9, 17, 34], "ii": 31, "ile106v": 23, "ile227_glu228inst": 23, "ile54thr": 23, "illustr": [23, 26], "img": 34, "immun": 31, "impair": 27, "implement": [4, 6, 10, 14, 17, 24, 26, 29, 33, 34, 37, 43, 44, 45], "implementor": 15, "impli": [7, 26, 32, 35], "implicitli": [32, 40], "import": [4, 6, 8, 15, 16, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 37, 38, 40, 43, 44, 45], "impos": 4, "imposs": [8, 10, 28], "imprecis": [15, 17], "imprecise_sv_functional_annot": 17, "imprecisesvfunctionalannot": [0, 17], "imprecisesvinfo": [0, 15, 17], "includ": [1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 19, 21, 23, 25, 26, 27, 28, 30, 33, 34, 36, 37, 39, 40, 44], "include_computational_tx": 17, "include_ontology_class_onset": 17, "include_patients_with_no_hpo": 15, "include_patients_with_no_vari": 15, "inclus": [6, 39, 45], "incomplete_terminal_codon_vari": 15, "increas": [23, 26, 30], "indel": 15, "indent": [14, 17], "independ": [15, 35], "index": [1, 6, 8, 10, 15, 22, 28, 31, 44], "indic": [1, 3, 15, 44], "indirect": [23, 26, 35], "individu": [1, 2, 3, 5, 6, 7, 8, 10, 11, 12, 15, 21, 23, 25, 26, 27, 28, 29, 30, 32, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45], "infer": 23, "inflammatori": 31, "info": [2, 3, 6, 15, 17, 23, 26, 30, 32, 45], "inform": [6, 10, 15, 19, 21, 23, 30, 33, 34, 35, 37, 41], "infram": 23, "inframe_delet": [15, 23, 30], "inframe_insert": [15, 23, 30], "ingest": 21, "inherit": [25, 35, 39], "inhibin": 31, "initi": [7, 15, 22], "inner": [6, 31], "input": [2, 17, 18, 19, 21, 23, 30, 33], "insert": [15, 17, 23, 32], "insight": [23, 31, 34], "instal": [21, 34], "instanc": [2, 4, 5, 6, 7, 8, 15, 17, 26, 27, 29, 30, 32, 34, 35, 36, 37, 40, 44, 45], "instanti": 34, "instead": [6, 15, 35, 37, 44], "instruct": [21, 25, 26, 27, 28, 45], "insulin": 31, "int": [1, 2, 3, 4, 5, 6, 15, 16, 17, 19], "integ": 15, "integr": [22, 30, 34], "integu": 31, "intellectu": [27, 37], "intend": [8, 15], "inter": [27, 41], "interact": [15, 19, 33], "interest": [6, 7, 15, 17, 23, 26, 30, 31, 33, 35, 44], "intergenic_vari": [15, 17], "intern": 15, "internet": 22, "interpret": [17, 18, 27, 39], "intersect": 16, "interspers": 15, "interv": 16, "intestin": 31, "intracrani": 31, "intraocular": 31, "intrauterin": 37, "introduct": 33, "intron": [15, 23], "intron_vari": [15, 17, 23, 30, 45], "inv": 15, "invers": [6, 15, 45], "investig": [7, 8, 10, 15, 23, 25, 43], "invoc": 22, "involv": [15, 23, 26, 34, 35], "io": [0, 15, 17, 18, 19, 25, 26, 27, 28, 30, 34, 45], "iobas": [15, 18, 19], "ion": [15, 31], "ip3": 15, "ipython": 30, "iqr": 27, "is_al": 15, "is_censor": [10, 28], "is_cod": [15, 34], "is_deceas": 15, "is_empti": 16, "is_femal": 15, "is_filtered_out": 2, "is_frameshift": [26, 44], "is_gest": 15, "is_in_exon3": 28, "is_large_imprecise_sv": 6, "is_mal": 15, "is_missens": [25, 44], "is_neg": 16, "is_observ": 15, "is_ok": 17, "is_pass": 2, "is_posit": 16, "is_postnat": 15, "is_pref": 15, "is_pres": 15, "is_provid": 15, "is_structur": 15, "is_structural_delet": 6, "is_structural_vari": 6, "is_unknown": 15, "islet": 31, "iso8601": 15, "iso8601pt": 15, "isoform": [15, 34], "issu": [2, 15, 17, 21, 23, 34, 41], "item": [1, 2, 3, 5, 17, 19, 32, 37], "iter": [1, 2, 3, 5, 6, 7, 8, 10, 12, 14, 15, 16, 17, 19, 35], "iter_cohort_phenopacket": [23, 34, 40], "its": [7, 11, 15, 19, 27, 32, 40, 41, 45], "j": 3, "jinja2": 19, "joint": 31, "jordan": 27, "json": [14, 15, 17, 25, 26, 27, 28, 30, 45], "jsondecod": 14, "jsonencod": 14, "jt": 29, "judgment": [31, 35], "jupyt": [19, 21, 30], "just": [15, 17, 19, 23, 25, 26, 34, 37], "juvenil": 17, "k": 44, "keep": 7, "kei": [6, 15, 21, 23, 30], "kidnei": [8, 27, 28], "kind": [17, 29, 33, 37], "know": [11, 15, 16, 17, 34], "known": [11, 15, 30, 40], "kwarg": 14, "lab": 25, "label": [6, 8, 11, 15, 19, 25, 28, 31, 34, 38], "label_summari": 15, "labeling_method": 19, "laboratori": 27, "lack": [7, 10, 17, 35], "lactat": 31, "lambda": 28, "langerhan": 31, "larg": [6, 15, 16, 17, 31], "larger": 15, "last": [10, 11, 13, 15, 23, 26, 27, 30], "last_menstrual_period": 15, "later": [25, 26, 27, 28, 33, 45], "latest": 23, "lead": [6, 15, 23, 26, 27, 31, 32, 35, 36, 45], "learn": [23, 26], "least": [2, 6, 17, 23, 26, 27, 35, 41, 44, 45], "leav": [21, 34], "left": 16, "legend": [10, 19, 25], "leigh": 15, "len": [15, 23, 25, 26, 27, 28, 30, 32, 34, 35, 40, 45], "length": [6, 15, 16, 27, 30, 33, 45], "lenient": 17, "lenti": [38, 40], "leptin": 31, "less": [1, 3, 6, 23, 26, 35], "let": [14, 15, 26, 27, 28, 32, 34, 35, 36, 44, 45], "letter": 34, "leu435argfster147": 23, "leu65glnfster10": 23, "leu94arg": 23, "leukocyt": 31, "level": [1, 3, 8, 15, 26, 27, 30, 31, 34, 45], "leverag": [2, 28, 30, 34, 37, 40, 45], "li": [16, 29], "librari": [0, 16, 22, 24, 34], "life": 26, "like": [14, 19, 21, 31, 35], "limb": [23, 26, 31], "limit": [2, 35, 37], "line": [15, 22, 27, 28], "lineag": 31, "link": 39, "lip": 37, "liposaccharid": 31, "list": [6, 7, 8, 14, 15, 23, 26, 31, 37, 40, 41], "list_all_diseas": 15, "list_all_protein": 15, "list_all_vari": 15, "list_measur": 15, "list_present_phenotyp": 15, "liter": [1, 3, 6, 11, 15, 17, 19, 32], "literatur": [6, 23], "liver": [8, 31], "ll": 34, "lmna": 36, "load": [14, 17, 30, 37, 40], "load_minimal_hpo": [23, 26, 27, 28, 30, 34, 35, 37, 40], "load_phenopacket": [0, 17, 23, 34, 40], "load_phenopacket_fil": [0, 17, 34], "load_phenopacket_fold": [0, 17, 34], "loader": 34, "local": [17, 18, 30], "locat": [15, 16, 17, 18, 21, 23, 30, 31, 34, 37, 45], "locu": [15, 44], "lof": 27, "lof_effect": 27, "lof_mut": 27, "log": [12, 28, 30, 42], "logic": [35, 37, 45], "logrank": [1, 12], "logranktest": [10, 12, 28], "loinc": [8, 15, 25], "long": 26, "loss": [15, 27, 44], "lost": 11, "lower": [26, 31, 45], "lump": 44, "ly": 27, "lymph": 31, "lymphat": 31, "lymphocyt": 31, "lys226asn": 23, "lys88ter": 23, "lysosom": 31, "m": [4, 15, 22], "macrocephali": 37, "macroscop": 31, "made": [23, 35], "magic": 30, "mai": [3, 8, 10, 15, 17, 26, 27, 30, 34, 35, 36, 44, 45], "main": [23, 27, 34], "major": [16, 41], "major_assembli": 16, "major_formatt": 28, "major_loc": 28, "make": [6, 30, 35], "male": [15, 23, 30, 43], "mandatori": 15, "mane": [15, 23, 25, 26, 27, 28, 34, 45], "mane_pt_id": 34, "mane_tx_id": 34, "mani": [23, 24, 30, 31, 33, 34, 35, 37, 40, 41, 45], "manifest": [21, 34], "mann": [8, 9, 24, 30, 33, 37, 42], "mannwhitneystatist": [8, 9, 27], "mannwhitneyu": [9, 27], "manual": [15, 26, 30], "map": [2, 15, 17, 19], "marfan": 38, "marker": [19, 31], "marker_count": 19, "marrow": 31, "mass": [8, 15, 25, 27, 31], "match": [6, 8, 11, 27, 39], "matern": 29, "math": 8, "matplotlib": [8, 10, 19, 23, 27, 28, 30, 34], "matrix": [2, 3], "matur": 31, "mature_mirna_vari": 15, "maxim": 41, "maximum": [2, 23, 26, 37], "me": 15, "mean": [15, 26, 27, 31, 35], "meaning": 5, "measur": [0, 8, 15, 23, 24, 27, 30, 31, 33], "measurement_by_id": 15, "measurementphenotypescor": [1, 8, 25, 27], "median": 27, "mediastinum": 31, "medic": [21, 31, 35], "medicin": 21, "meet": [6, 15, 27, 39, 45], "megakaryocyt": 31, "member": [10, 15, 17, 23, 26, 28, 30, 34, 35], "membran": 31, "mendelian": 21, "menstrual": 15, "mental": 31, "mesenteri": 31, "messag": 14, "met": 45, "met74il": 23, "met83phefster6": 23, "meta_label": [15, 34], "metabol": 31, "metabolit": 31, "metadata": [17, 19], "metaphysi": 31, "method": [2, 3, 6, 7, 14, 15, 16, 17, 23, 26, 27, 34, 35], "mhc": 31, "micro": 37, "microcephali": 37, "middl": 31, "midfac": 37, "midpoint": 17, "midwif": 15, "might": [29, 30], "mild": [37, 44], "mim": 23, "miner": 31, "minimalontologi": [2, 3, 7, 8, 11, 17, 19, 40], "minimalterm": 15, "minimum": 2, "mininum": 35, "miss": [10, 11, 17, 41], "missens": [1, 2, 3, 6, 15, 21, 25, 26, 27, 29, 32, 35, 39, 44, 45], "missense_and_exon20": 45, "missense_or_nonsens": 45, "missense_vari": [1, 3, 6, 15, 23, 25, 27, 30, 44, 45], "missing_implies_exclud": 7, "missing_implies_phenotype_exclud": 7, "mitig": [26, 35], "mitochondrion": 31, "mixin": [1, 16], "mnv": 15, "mode": [17, 35, 39], "model": [0, 2, 6, 18, 23, 25, 26, 27, 28, 30, 32, 34, 44, 45], "moder": 37, "modifi": 35, "modul": [0, 15, 16, 26, 27, 30, 34], "moment": 17, "monarch": 22, "mondo": 7, "monoallel": [6, 28], "monoallelic_pred": [5, 6, 23, 26, 27, 28, 44], "monophenotypeanalysisresult": [0, 1, 8, 10], "month": 15, "more": [1, 2, 3, 6, 8, 9, 12, 15, 17, 19, 22, 23, 26, 27, 30, 31, 33, 34, 37, 38, 44, 45], "morpholog": 31, "morphologi": [8, 21, 23, 26, 27, 30, 31, 32, 35, 37, 40], "mortal": 30, "most": [15, 16, 19, 23, 30, 31, 34, 35, 41], "mostli": [15, 41], "motif": [15, 21], "motil": 31, "motor": [23, 31], "movement": 31, "mpl": 28, "mri": 31, "mt": [2, 23, 26, 33], "mtc": [2, 3, 19, 23, 26, 31, 33, 35], "mtc_alpha": [3, 26], "mtc_correct": [1, 3, 26, 35], "mtc_filter": [1, 3, 26, 35], "mtc_filter_nam": 3, "mtc_filter_result": 3, "mtc_issu": 2, "mtc_report": [23, 26], "mtc_viewer": [23, 26], "mtcstatsview": [0, 19, 23, 26], "much": [2, 30, 31, 35, 45], "mucociliari": 31, "mucosa": 31, "mucu": 31, "multi": [15, 45], "multiphenotypeanalysi": [1, 3], "multiphenotypeanalysisresult": [0, 1, 3], "multipl": [1, 2, 3, 23, 26, 31, 33, 45], "multipleloc": 28, "multipli": 35, "muscl": 31, "muscular": 26, "musculatur": 31, "musculoskelet": 31, "must": [2, 3, 5, 6, 7, 8, 10, 15, 17, 22, 26, 27, 30, 34, 38, 41, 44, 45], "mutat": [23, 25, 26, 27, 28, 30, 34, 40, 44, 45], "mutlipl": 35, "myelin": 31, "myeloid": 31, "n": [2, 4, 6, 15, 23, 30, 31, 40], "n_categor": 5, "n_filtered_out": 3, "n_significant_for_alpha": [1, 3], "n_usabl": [1, 2, 3], "nacgtacgtac": 15, "nail": 31, "name": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 15, 16, 17, 18, 25, 27, 28, 30, 34, 38, 40, 44], "nan": [1, 3, 8, 9, 10, 25, 27], "nanogram": 15, "nasal": 31, "natur": 15, "nc_000001": 16, "ncbi": [23, 29], "ncit": 15, "ndarrai": 19, "neck": 31, "need": [15, 17, 23, 26, 28, 33, 34, 35, 40, 44], "neg": [6, 15, 16, 17, 32], "neoplasm": 31, "neopterin": 31, "neq": 44, "nerv": 31, "nervou": [31, 32, 35], "net": 15, "network": 34, "neuron": 31, "never": [16, 35], "new": 19, "next": [23, 34, 36, 45], "ng": 15, "nih": 29, "nippl": 31, "nlm": 29, "nm_000500": 25, "nm_001042681": [27, 45], "nm_002834": 17, "nm_003361": 28, "nm_005912": 17, "nm_013275": 45, "nm_123": 6, "nm_1234": [6, 44], "nm_123456": [1, 3, 6, 15], "nm_170707": 15, "nm_181486": [23, 26, 30, 34], "nmd_transcript_vari": 15, "no_cal": 15, "no_genotype_has_more_than_one_hpo": 2, "node": 31, "nomin": [1, 3, 23, 26, 35], "non": [2, 3, 6, 10, 15, 17, 23, 26, 27, 35, 45], "non_coding_transcript_exon_vari": [15, 17], "non_coding_transcript_vari": [15, 17], "non_frameshift_del": 45, "non_frameshift_effect": 45, "non_frameshift_pred": 45, "non_specified_term": 2, "noncoding_effect": 17, "none": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 19, 23, 27, 28, 34, 35, 37, 41, 44], "nonfaci": 37, "nons": 29, "nonsens": [2, 3, 6, 25, 26, 29, 35, 45], "normal": 21, "nose": 37, "notat": [15, 32], "note": [2, 3, 7, 13, 15, 16, 23, 26, 34, 37, 38, 43, 44, 45], "notebook": [19, 21, 30], "notepad": 17, "noth": 45, "novel": 15, "now": [15, 23, 25, 26, 27, 28, 34, 35, 40, 44], "np_": 23, "np_000129": 15, "np_001027558": 17, "np_001027559": 15, "np_037407": 17, "np_852259": [23, 30, 34], "nuclear": 15, "nucleobas": 31, "nucleotid": [15, 23, 32, 45], "nucleu": 35, "nul": 15, "null": 35, "number": [1, 2, 3, 4, 5, 6, 8, 15, 16, 23, 26, 27, 28, 31, 35, 37], "numer": [15, 30], "o": [14, 17], "obj": 14, "object": [1, 2, 3, 6, 8, 10, 14, 15, 16, 17, 19, 34], "object_hook": 14, "observ": [2, 8, 15, 21, 23, 26, 30, 40], "observablefeatur": 15, "obtain": [15, 17, 23, 34, 35, 37], "obvious": 30, "occipitofrontali": 31, "occur": [15, 23, 27, 30, 34], "occurr": 23, "oddsratio": 26, "odontoid": 31, "off": [41, 45], "offer": [24, 30, 35, 37, 42, 45], "offlin": 17, "often": 15, "ok": [2, 17], "oldest": 35, "omim": [7, 8, 38], "omit": [2, 23, 26, 35, 38, 41, 43, 44], "onc": [15, 26, 34], "one": [2, 5, 6, 7, 8, 15, 17, 22, 23, 26, 27, 28, 29, 30, 31, 34, 36, 37, 41, 44], "one_genotype_has_zero_hpo_observ": 2, "ones": 17, "onli": [2, 5, 6, 7, 15, 17, 23, 26, 29, 30, 35, 40], "onlin": 22, "only_hgv": 19, "onset": [10, 11, 15, 17, 23, 28, 30, 31, 32], "onsetawar": 15, "onto": 19, "ontologi": [2, 3, 7, 15, 17, 21, 23, 32, 34, 37], "ontology_class": 17, "ontologyclass": 17, "oocyt": 31, "open": [18, 25, 26, 27, 28, 30, 34, 41, 45], "open_phenopacket_stor": [23, 34, 40], "open_resourc": [0, 18], "open_text_io_handle_for_read": [0, 18], "open_text_io_handle_for_writ": [0, 18], "oper": [6, 15, 45], "oppos": 15, "opposit": 16, "option": [2, 6, 7, 15, 17, 22, 23, 34, 35, 40, 44], "oram": [23, 30, 45], "order": [2, 15, 23, 26, 30, 34, 44], "organ": [15, 27, 31], "orgogozo": 21, "origin": 37, "orthogon": 39, "osmol": 31, "osteocalcin": 31, "other": [2, 15, 16, 17, 19, 21, 23, 25, 26, 28, 29, 34, 35, 36, 37, 39, 44], "otherwis": [6, 7, 10, 15, 37], "our": [23, 24, 26, 28, 31, 35, 37, 41], "out": [2, 3, 5, 16, 17, 23, 26, 27, 28, 32, 34, 35], "outcom": [1, 3], "outer": [6, 31], "output": [17, 18, 19], "over": 15, "overal": [2, 35], "overlap": [3, 6, 15, 16, 19, 23, 28, 45], "overlapping_exon": 15, "overlaps_with": [15, 16], "overlaps_with_fifth_aa": 6, "overlaps_with_first_20": 6, "overload": [15, 45], "overrepres": 15, "overview": [23, 24, 30], "own": 16, "p": [1, 2, 3, 4, 7, 8, 9, 12, 15, 19, 21, 23, 26, 30, 34, 35, 40, 45], "p10y": 15, "p10y4m2d": 15, "p13": [16, 17], "p13_assembly_report": 18, "p22w3d": 15, "p2w6d": 15, "p_valu": [26, 27], "packag": [18, 20, 21, 22, 35], "page": [15, 23, 30, 33, 41], "pair": [3, 4, 6, 12, 15, 32], "pancrea": 31, "pancreat": 31, "panda": [2, 15, 34], "param": [6, 15, 16, 17, 18], "paramet": [1, 2, 3, 5, 6, 7, 8, 10, 12, 14, 15, 16, 17, 18, 19], "parametr": 27, "parathyroid": 31, "parent": [3, 17, 35, 37], "pars": [15, 17], "parse_multipl": 17, "parse_respons": 17, "parse_uniprot_json": 17, "parser": 17, "part": [1, 15, 19, 34, 37], "particular": 30, "partit": [1, 5, 6, 7, 8, 10, 25, 36, 41, 43], "pass": [2, 6, 14, 15, 32, 35], "past": 35, "patch": [8, 16], "patern": 29, "path": [13, 15, 17, 18, 19, 23, 26, 33, 34, 40], "pathogen": [23, 34, 45], "patient": [0, 1, 2, 3, 5, 6, 7, 8, 10, 15, 17, 19, 21, 23, 26, 27, 34, 35, 36, 40, 41], "patient_1": 10, "patient_2": 10, "patient_3": 10, "patient_4": 10, "patient_cr": 17, "patient_id": [10, 15, 25, 27, 28], "patientcategori": [5, 7], "patientcr": [0, 17], "pattern": 31, "payload": 17, "pcat": [1, 23, 26, 35], "pd": [15, 34], "pediatr": 17, "pehnotyp": 2, "peptid": 31, "per": 15, "percent": [23, 26], "percentag": 35, "perform": [4, 15, 17, 21, 23, 26, 27, 29, 30, 33, 34, 35], "perifollicular": 31, "period": 15, "peripher": 31, "peritoneum": 31, "permiss": [17, 34], "peroxisom": 31, "persist": [25, 26, 27, 28, 33, 45], "ph": [30, 31], "ph_col": 1, "ph_predic": 2, "phagocytosi": 31, "phe168leufster6": 23, "pheno_pred": [1, 3, 23, 26, 40], "pheno_scor": [8, 25, 27, 37], "phenopacket": [15, 17, 21, 23, 25, 26, 27, 28, 30, 33, 40, 45], "phenopacket1": 34, "phenopacket2": 34, "phenopacket_registri": 23, "phenopacketontologytermonsetpars": [0, 17], "phenopacketpatientcr": [0, 17], "phenopacketvariantcoordinatefind": [0, 17], "phenotyp": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 17, 21, 24, 28, 30, 31, 33, 37, 39, 41, 45], "phenotype_by_id": 15, "phenotype_cr": 17, "phenotype_scor": [8, 27], "phenotypecategor": [5, 7], "phenotypemtcfilt": [1, 2, 3, 23, 35], "phenotypemtcissu": [1, 2], "phenotypemtcresult": [1, 2, 3], "phenotypepolypred": [1, 2, 3, 5, 7, 41], "phenotypescor": [1, 8, 9], "phenotypescoreanalysi": [1, 8, 25, 27, 28], "phenotypescoreanalysisresult": [1, 8], "phenotypescorestatist": [8, 9], "phenotypic_abnorm": 2, "phosphat": 31, "physician": 15, "physiolog": 31, "physiologi": [21, 31, 32], "pick": 26, "pickl": 17, "piec": 15, "piezo1": 34, "pineal": 31, "pinna": 37, "pip": 22, "pituitari": 31, "place": [21, 34], "placent": 31, "placenta": 31, "plan": 30, "plasma": [8, 15, 25, 27], "plate": 34, "platelet": 31, "platform": 18, "platysma": 31, "pld1": 30, "pleas": [30, 41], "plot": [8, 10, 19, 28, 33], "plot_boxplot": [8, 27], "plot_kaplan_meier_curv": [10, 28], "plt": [19, 23, 27, 28, 30, 34], "plu": [6, 15], "pm": [23, 34], "pm_servic": 30, "pmid": 23, "pmid_22034507_aii_1": 28, "pmid_22034507_aii_2": 28, "pmid_22034507_aii_3": 28, "pmid_22034507_aii_5": 28, "pmid_22034507_aiii_4": 28, "pmid_27087320_subject_1": 27, "pmid_27087320_subject_10": 27, "pmid_27087320_subject_2": 27, "pmid_29330883_subj": 34, "pmid_29330883_subject_1": 27, "pmid_29330883_subject_2": 27, "pmid_30968594_individual_10": 25, "pmid_30968594_individual_11": 25, "pmid_30968594_individual_12": 25, "pmid_30968594_individual_13": 25, "pmid_30968594_individual_14": 25, "png": 34, "po": [15, 16, 28, 32], "point": [15, 17, 27, 34, 37], "point_mut": 27, "point_mutation_effect": 27, "polar": [34, 35], "polici": [17, 23, 34], "polypred": [1, 5, 6, 7], "pore": 34, "port": 16, "posit": [3, 6, 15, 16, 17, 23, 26, 30, 32, 35], "posixpath": 13, "possibl": [2, 3, 5, 8, 29, 30, 34, 43], "possible_result": 2, "possibli": 39, "posterior": [31, 35], "postnat": [11, 15], "postnatal_dai": 15, "postnatal_year": 15, "potassium": 30, "potenti": [27, 33], "power": [33, 35, 41], "pp": 17, "pp_dir": 34, "pp_directori": 17, "pp_file": 17, "pp_file_path": 34, "ppktstore": [23, 34, 40], "practic": 29, "pre": [2, 3], "precis": 21, "precursor": 31, "predic": [1, 2, 3, 4, 8, 10, 33, 36, 38, 43], "predict": [6, 15, 23, 26, 27, 30, 34, 44, 45], "predictor": [17, 34], "prefer": [15, 30], "preimplant": 31, "prematur": 21, "prenat": 31, "prepar": [3, 6, 7, 15, 17, 25, 26, 27, 28, 34, 36, 45], "prepare_hpo_terms_of_interest": [5, 7], "prepare_predicates_for_terms_of_interest": [5, 7, 23, 26, 40], "preprocess": [0, 15, 23, 30, 34, 40], "preprocessingvalidationresult": [0, 17, 34], "preproprotein": 15, "prerequisit": 37, "presenc": [1, 3, 6, 7, 15, 23, 26, 27, 30, 34, 35, 36, 39, 40, 45], "present": [1, 3, 7, 8, 15, 16, 19, 23, 26, 27, 30, 37, 38, 44], "present_diseas": 15, "present_phenotyp": 15, "present_phenotype_categor": 7, "present_phenotype_categori": 7, "pressur": 31, "pretti": 19, "prevent": [2, 3, 45], "previou": [35, 44], "previous": 26, "primari": [15, 31, 45], "principl": 29, "print": [15, 17, 34], "pro139glnfster11": 23, "pro14thr": [23, 30], "pro85thr": 23, "probabl": [26, 35], "problem": 35, "proce": 17, "procedur": [23, 26, 31, 33], "process": [17, 19, 23, 26, 30, 34, 40], "process_respons": 17, "produc": [1, 2, 4, 5, 7, 8, 30], "product": 19, "profound": 37, "programmat": [6, 17], "programmaticali": 34, "project": 15, "prolifer": 31, "prong": [26, 41], "pronounc": 21, "propagatingphenotypepred": 7, "properti": [1, 2, 3, 4, 5, 7, 8, 10, 15, 16, 17, 19], "proport": 35, "protcachingmetadataservic": [0, 17], "protein": [6, 15, 16, 17, 19, 21, 31, 33, 45], "protein_altering_vari": 15, "protein_cach": 17, "protein_effect_coordin": 15, "protein_effect_end": 15, "protein_effect_loc": 15, "protein_effect_start": 15, "protein_featur": [6, 15, 34], "protein_feature_end": 19, "protein_feature_nam": 19, "protein_feature_start": 19, "protein_feature_typ": [6, 19], "protein_id": [15, 17, 19, 34], "protein_length": [15, 19, 34], "protein_meta": [15, 19, 23, 30, 34], "protein_metadata": [6, 19, 30], "protein_sourc": 17, "proteinannotationcach": [0, 17], "proteinfeatur": [0, 15], "proteinmetadata": [0, 6, 15, 17, 19, 23, 34], "proteinmetadataservic": [0, 17, 34], "proteinpred": 41, "proteinvariantview": [0, 19, 30], "proteinvisu": [0, 19, 23, 30, 34], "proteinvisualiz": [0, 19, 34], "provid": [1, 2, 3, 6, 7, 8, 10, 11, 12, 15, 16, 17, 19, 21, 23, 24, 27, 30, 33, 35, 37, 40, 41, 44], "proxi": 37, "pscore": [1, 25, 27, 37], "pt_id": 30, "public": 37, "publish": [22, 40], "pubm": 29, "pulmonari": 31, "pupillari": 31, "purin": 31, "purpos": [2, 25, 26, 28, 30, 34, 35, 45], "put": [15, 25, 27, 28], "putamen": 35, "pval": [1, 3, 25, 27, 28], "pval_kind": [1, 3], "pvalu": 27, "pvi": [19, 34], "px": 30, "px_id": 23, "py": 15, "pydoc": 34, "pypi": 22, "pyplot": [23, 27, 28, 30, 34], "pyrimidin": 31, "pytest": 22, "python": [4, 14, 21, 22, 26, 30, 34, 35, 45], "python3": 22, "q": [23, 34], "q1": 27, "q3": 27, "q99593": 34, "qc_result": 34, "qual": [15, 32], "qualnam": [15, 16], "quartil": 27, "queri": [7, 8, 15, 17, 27, 34, 40], "question": [6, 21, 24, 45], "r": 27, "radiu": [23, 26, 30], "rais": [5, 14, 15, 16, 17], "random": [4, 15], "random_se": 19, "rang": [2, 15, 17, 27, 37], "rank": [9, 12, 27, 28, 30, 42], "rare": [0, 2, 23, 34, 40], "rate": [23, 31, 35], "rather": 31, "ratio": 31, "re": 15, "reach": 17, "read": [18, 19, 21, 45], "readabl": [15, 19], "reader": 34, "readi": [15, 23], "readili": 34, "real": [25, 26], "realiz": 35, "realli": 34, "reason": [2, 23, 26, 31, 34], "receiv": 23, "receptor": 34, "recess": 44, "recommend": [2, 6, 15, 21, 23, 26, 30, 34, 35, 40], "record": [15, 23, 30, 40], "red": [27, 31], "redox": 31, "reduc": [2, 23, 26, 34, 35], "redund": 35, "ref": [6, 15, 19, 32], "ref_length": [6, 27], "refer": [6, 15, 21, 27, 31, 33, 34, 37], "reflect": 41, "reflex": 31, "refract": 31, "refseq": [15, 16, 17, 34], "refseq_nam": 16, "regard": [2, 10, 15, 19, 23, 30], "regardless": 15, "region": [6, 15, 16, 19, 23, 30, 32, 34, 45], "registri": [23, 34, 40], "regul": [30, 31], "regulatory_region_abl": 15, "regulatory_region_amplif": 15, "regulatory_region_vari": 15, "rel": [6, 37], "relat": 35, "relationship": [21, 26], "releas": [23, 26, 27, 28, 30, 31, 34, 35, 37, 40], "relev": [2, 15, 23, 27, 34], "remot": [17, 34], "remov": [6, 31, 32, 45], "renal": [27, 28], "renin": 31, "repair": 31, "repeat": 15, "replac": 45, "report": [1, 3, 8, 10, 15, 17, 19, 21, 23, 25, 26, 27, 28, 30, 40], "repositori": 22, "repres": [1, 2, 3, 5, 6, 7, 8, 10, 15, 16, 17, 19, 21, 27, 34, 35], "represent": [15, 17], "reproduct": 31, "request": 17, "requir": [1, 4, 10, 15, 22, 23, 41], "requisit": 34, "rere": [27, 34, 45], "rere_mane_tx_id": 45, "residu": [6, 15, 30, 34], "resolut": 15, "resourc": [6, 15, 17, 18, 34], "respect": [3, 10, 15, 26, 32, 33, 34, 44, 45], "respir": 31, "respiratori": 31, "respons": [17, 27, 31, 34], "rest": [15, 17, 25, 31], "restrict": 29, "result": [1, 2, 3, 8, 10, 15, 17, 19, 21, 23, 25, 26, 27, 28, 30, 31, 34, 35, 40, 41, 45], "retain": 35, "retainin": 23, "reticulocyt": 31, "retriev": [15, 16, 17], "return": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 35, 41], "reus": 44, "revers": 16, "right": [16, 19], "risk": 26, "rna": 16, "root": [2, 31, 35], "row": [1, 2, 3, 23], "rule": [5, 11, 23, 26, 30, 33, 40, 45], "run": [17, 25, 27, 28, 34], "runner": 17, "runonlin": 22, "rust": 15, "sai": 35, "salient": [19, 30], "salivari": 31, "same": [2, 3, 6, 12, 15, 16, 23, 26, 27, 31, 32, 34, 35, 37, 44], "same_count_as_the_only_child": 2, "sampl": [12, 15, 23], "sample_id": 15, "samplelabel": [0, 15], "sapien": 6, "save": 34, "savefig": 34, "scalp": 31, "scenario": 5, "schema": [15, 17, 19, 26, 34], "scienc": 6, "scientif": 30, "scipi": [4, 9, 12, 26, 27], "scipyfisherexact": 3, "sclera": 31, "score": [1, 8, 9, 12, 24, 30, 33, 42], "score_analysi": [25, 27], "score_statist": [8, 25, 27], "scorer": [8, 27], "screenshot": 34, "search": [17, 23, 31, 34, 41], "sebac": 31, "second": [6, 17, 30], "secondari": 15, "secret": 31, "section": [2, 3, 6, 7, 8, 15, 17, 23, 25, 26, 27, 28, 30, 35, 44, 45], "secundum": [23, 26, 30], "sediment": 31, "see": [2, 3, 6, 7, 8, 9, 10, 15, 19, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 44, 45], "seek": 39, "seem": 41, "seen": [15, 27, 35], "segment": [15, 31, 40], "segreg": 31, "seizur": [23, 32], "select": [2, 6, 10, 23, 26, 27], "self": [14, 16], "sens": [30, 31, 35], "sensat": 31, "sensibl": 30, "sensori": 31, "sensorineur": 27, "separ": [14, 26, 42], "septal": [23, 26, 30, 32], "septum": [23, 26, 32], "sequenc": [1, 2, 3, 4, 5, 6, 7, 9, 12, 15, 16, 17, 19, 33, 34], "sequence_vari": 15, "ser196ter": 23, "ser261ci": [23, 30], "ser36thrfster25": [23, 30], "serial": [25, 26, 27, 28, 45], "serializ": 14, "serum": [8, 15, 25, 27, 31], "serv": 41, "servic": 17, "set": [2, 8, 13, 15, 23, 26, 27, 28, 35, 36, 40, 44], "setup": [26, 30, 35], "sever": [3, 5, 15, 23, 25, 26, 27, 30, 32, 34, 35, 37, 42, 44, 45], "sex": [0, 6, 7, 8, 15, 23, 30, 31, 33, 39], "sex_pred": [5, 6, 43], "sh": 35, "shape": 37, "sharpei": 31, "shelf": [27, 41, 45], "shift": 45, "ship": 34, "short": [15, 23, 26, 30, 37], "shortcut": 15, "shorter": [6, 26], "should": [2, 3, 6, 7, 13, 15, 16, 17, 19, 23, 25, 27, 34], "show": [15, 19, 25, 26, 27, 28, 30, 31, 32, 34, 35, 40, 41, 45], "shown": [33, 34], "sidak": 35, "side": [4, 12, 27], "sign": [15, 16, 23, 25, 26, 27], "signal": [31, 35], "signific": [1, 3, 15, 26, 27, 31, 35, 37], "significant_phenotype_indic": [1, 3], "significantli": [23, 26, 27], "sime": 35, "similar": [15, 27, 44], "similarli": [10, 40, 44], "simpl": [6, 22, 29, 32, 34, 37, 45], "simplest": 35, "simpli": [2, 35], "simplifi": [23, 26], "sinc": [3, 6, 15, 27], "sine": 15, "singl": [1, 2, 15, 23, 36, 45], "situ": 31, "size": [2, 15, 16, 30, 31], "skelet": 31, "skeleton": [23, 26], "skin": [8, 31], "skinfold": 31, "skip": [2, 23, 26, 31], "skipkei": 14, "skipping_general_term": 2, "skipping_non_phenotype_term": 2, "skipping_since_one_genotype_had_zero_observ": 2, "skull": 31, "slice": 16, "small": [15, 32, 35, 37], "smell": 31, "snv": [15, 32, 45], "so": [6, 15, 27, 34, 35, 45], "so_term": 15, "softwar": 24, "sole": 26, "solut": 34, "somat": 31, "some": [1, 4, 17, 21, 22, 30, 34, 35, 36, 41], "some_cell_has_greater_than_one_count": 2, "sometim": [36, 44, 45], "sort": [15, 17], "sort_index": [25, 27, 28], "sort_kei": 14, "sound": [31, 40], "sourc": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 45], "span": [6, 15, 16, 31, 32, 34], "specif": [3, 6, 15, 17, 21, 23, 27, 28, 30, 31, 34, 35, 40], "specifi": 2, "specified_term": 35, "specifiedtermsmtcfilt": [1, 2, 35], "specifytermsstrategi": 26, "spell": 32, "spinal": 31, "spleen": 31, "splice": [15, 23], "splice_acceptor_vari": [15, 17, 23, 30], "splice_donor_5th_base_vari": [15, 17, 23, 30], "splice_donor_region_vari": 15, "splice_donor_vari": [15, 17, 23, 30], "splice_polypyrimidine_tract_vari": [15, 17], "splice_region_vari": [15, 23, 30], "spuriou": 35, "st1": 2, "stabil": [15, 31], "stage": [15, 28], "stalk": 31, "standalon": 19, "standard": [15, 33], "start": [6, 15, 16, 17, 19, 27, 30, 31, 34, 44], "start_lost": [15, 27], "start_on_strand": 16, "start_retained_vari": 15, "stat": [3, 8, 10, 25, 26, 27, 28, 35], "state": [15, 32], "static": [2, 6, 8, 14, 15, 17, 35], "statist": [0, 1, 3, 4, 8, 9, 10, 12, 21, 23, 31, 33, 35, 37, 41], "statistic_result": [1, 3, 8, 10], "statisticresult": [0, 1, 3, 4, 8, 9, 10, 12], "statsmodel": 35, "statu": [0, 2, 11, 15, 23, 30], "statur": 37, "stdout": 17, "step": [22, 23, 26, 33, 34, 39], "stimul": 31, "stomatocytosi": 34, "stool": 31, "stop": [23, 31], "stop_gain": [6, 15, 23, 27, 30, 45], "stop_lost": 15, "stop_retained_vari": [15, 23, 30], "storag": 17, "store": [1, 8, 15, 17, 19, 23, 26, 27, 28, 30, 34, 35, 37, 40], "store_annot": 17, "str": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 32, 34], "strabismu": 26, "strand": [6, 15, 16, 34], "strategi": [2, 19, 26, 31], "stress": 31, "strict": 17, "string": [8, 15, 17, 19, 31], "stringio": 17, "stromal": 31, "strongli": [6, 15], "structur": [6, 10, 15, 26, 27, 30, 31, 32, 35, 37, 45], "structural_defect": 27, "structural_so_id_to_displai": 15, "structural_typ": [6, 15, 45], "structural_vari": 6, "student": 15, "studi": [11, 21, 28], "stump": 31, "sub": [15, 26, 34], "subclass": [6, 14], "subgroup": 15, "subject": [15, 27, 34, 40], "submodul": 20, "subpackag": 20, "subplot": [23, 27, 28, 30, 34], "subsect": 15, "subsequ": [26, 34], "subunit": 31, "successfulli": [23, 30], "suffix": [17, 34], "suggest": 30, "suitabl": 15, "sum": [27, 37, 44], "sum_": 44, "summar": [5, 15, 17, 19, 32, 34], "summari": [5, 17, 33, 34], "summarize_group": [5, 6], "summarize_hpo_analysi": [0, 19, 23, 26], "summary_df": [23, 26], "suox": 29, "super": 14, "supercoil": 15, "suppli": 15, "support": [6, 14, 15, 16, 21, 29, 45], "supports_shap": 4, "suppos": 14, "suppresor": 15, "surf1": [6, 15], "surf2": 6, "surfac": 31, "surviv": [1, 10, 11, 12, 24, 33, 35, 36, 42], "survival_analysi": 28, "survival_statist": 28, "survivalanalysi": [1, 10, 28], "survivalanalysisresult": [1, 10], "survivalmetr": 12, "survivalstatist": [10, 12], "sv": [6, 15, 17, 25], "sv_delet": 32, "sv_info": 15, "svart": 16, "svlen": [15, 32], "svtype": [15, 32], "sweat": 31, "switch": 22, "symbol": [6, 15, 16, 23, 32, 34, 36], "symptom": [15, 23, 25, 26, 27, 31], "synapt": 31, "syndrom": [15, 23, 30, 38, 45], "synonym": 45, "synonymous_vari": [15, 45], "system": [15, 16, 31, 32, 35, 37], "t": [9, 15, 17, 19, 23, 25, 30, 32], "tabl": [4, 19, 23, 26, 30, 31, 32, 33, 35, 44], "tail": 26, "take": [4, 6, 8, 17, 23, 26, 34, 35, 36, 38, 40], "tall": 37, "tandem": 15, "target": [3, 6, 7, 11, 30, 34, 36, 38, 45], "tast": 31, "taxon": 6, "tbx5": [30, 34, 40], "tbx5_gpsea_with_uniprot_domain": 34, "technic": 21, "tediou": [40, 45], "tedium": 40, "temperatur": 31, "templat": 19, "tempor": [1, 15, 28], "ten": [15, 35], "tend": 15, "term": [1, 2, 3, 7, 8, 11, 15, 17, 19, 21, 23, 25, 26, 27, 28, 30, 32, 33, 37, 40, 41], "term_frequency_threshold": [2, 26, 35], "term_id": [8, 11, 15, 25, 28], "term_id_to_ag": 17, "term_onset_pars": 17, "termid": [2, 3, 6, 7, 8, 11, 15, 40], "termin": [15, 21], "terms_to_test": [2, 35], "test": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 16, 17, 19, 21, 23, 24, 29, 31, 33, 37, 39, 40, 41, 42, 45], "test_nam": 15, "test_result": 15, "test_term_id": 15, "test_uniprot_json": 15, "testabl": 30, "testosteron": [8, 15, 25, 27], "text": 18, "textio": [5, 17, 18], "textiowrapp": [17, 18], "tf_binding_site_vari": 15, "tfbs_ablat": 15, "tfbs_amplif": 15, "th": 3, "than": [1, 2, 3, 6, 15, 23, 26, 27, 31], "thank": 26, "thei": [16, 21, 24, 26, 27, 31, 35, 45], "them": 30, "themselv": 16, "therebi": 2, "therefor": [2, 3, 6, 26, 31, 35, 45], "thi": [1, 2, 3, 6, 7, 8, 11, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 39, 40, 43, 44, 45], "thick": 31, "thin": 4, "thing": 30, "think": 35, "third": 27, "thorac": 31, "those": [36, 44], "thr161pro": 23, "thr223met": [23, 30], "thr72ly": 23, "three": [6, 15, 29, 35, 44], "three_prime_utr_vari": [15, 17], "threshold": [2, 6, 23, 26, 35], "thrombocyt": 31, "thrombosi": 31, "through": [15, 34], "thu": [1, 3, 15, 30, 35, 37], "thumb": [5, 23, 26, 30, 45], "thymu": 31, "thyroid": 31, "tick": 28, "ticker": 28, "tight_layout": 34, "tild": 45, "time": [3, 11, 15, 17, 22, 26, 28, 34, 35], "timelin": [0, 11, 15], "timeout": 17, "tissu": 31, "tl": 26, "to_displai": 15, "to_negative_strand": 16, "to_opposite_strand": 16, "to_positive_strand": 16, "to_str": 15, "todo": [19, 25, 29, 34, 39, 41, 42], "togeth": [15, 25, 27, 28], "tonsil": 31, "too": 31, "toolkit": [8, 17, 23, 34, 37], "top": [3, 7, 8, 15, 23, 27, 30, 31, 34], "top_phenotype_count": 19, "top_variant_count": 19, "total": [1, 3, 15, 23, 26, 27, 30, 35, 37], "total_patient_count": 15, "total_test": [1, 3, 23, 26], "track": 7, "tracker": [21, 41], "tract": 31, "trans_id": 15, "transcript": [1, 3, 6, 15, 17, 19, 23, 25, 26, 27, 28, 30, 33, 44, 45], "transcript_abl": [15, 27], "transcript_amplif": 15, "transcript_coordin": 19, "transcript_id": [6, 15, 19, 23, 30], "transcriptannot": [0, 15, 17], "transcriptcoordin": [0, 15, 17, 19, 23, 34], "transcriptcoordinateservic": [0, 17], "transcriptinfoawar": [0, 15, 17], "transform": [17, 34], "transit": 16, "translat": 15, "transloc": [6, 15], "transmiss": 31, "transpos": [15, 16], "transpose_coordin": [15, 16], "trascript": 23, "tri": 17, "triphalang": [23, 26, 30], "triphosph": 31, "trp121gly": [23, 30], "true": [2, 6, 7, 10, 14, 15, 16, 17, 19, 23, 26, 28, 30, 33, 34, 35, 40, 45], "truli": 30, "truncat": 23, "try": [13, 14, 16, 17], "tsv": 18, "ttest_ind": 9, "tteststatist": [8, 9, 25], "tupl": [3, 6, 8, 9, 15, 17, 23, 34, 35, 36, 40], "turn": [17, 34], "tutori": [21, 26, 33], "twice": 35, "two": [1, 3, 4, 6, 8, 12, 15, 16, 18, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 41, 44], "tx": [17, 19, 45], "tx_annot": 15, "tx_coordin": [19, 23, 30, 34], "tx_id": [6, 15, 17, 19, 23, 25, 26, 27, 28, 30, 44, 45], "tx_servic": 30, "txc_servic": [23, 34], "type": [1, 2, 3, 6, 7, 8, 14, 15, 16, 17, 19, 21, 33, 34, 35, 45], "typeerror": 14, "typic": [3, 15, 26, 39, 41], "tyr136ter": [23, 30], "tyr291ter": [23, 30], "tyr342thrfster52": [23, 30], "tyr407ter": [23, 34], "u": [8, 9, 23, 24, 26, 30, 33, 34, 37, 44, 45], "ucsc": 16, "ucsc_nam": 16, "ucum": 15, "umbil": 31, "umbilicu": 31, "umod": 28, "unambigu": 38, "unavail": 15, "under": [17, 23, 34, 35], "underli": 45, "undoubtedli": 34, "uniform": 6, "uninterest": 31, "uniprot": [15, 17, 30], "uniprot_json": [15, 34], "uniprotproteinmetadataservic": [0, 15, 17], "uniqu": [2, 3, 15, 23, 30], "unit": [15, 16, 22, 30], "unknown": [6, 15, 23, 30], "unknown_sex": [15, 43], "unless": [7, 23, 34, 35, 40], "unlik": [31, 35], "unnecessari": 31, "unsur": 30, "untest": [1, 3], "until": [11, 28], "untransl": [15, 34], "up": [23, 27, 35, 37, 40], "upper": [23, 26, 31], "upstream": 16, "upstream_gene_vari": [15, 17], "urat": 31, "uri": 15, "urin": 31, "urinari": 31, "urobilinogen": 31, "us": [1, 2, 3, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 39, 40, 41, 44, 45], "usabl": [1, 3], "usag": [6, 7, 9, 19, 45], "use_al": 35, "usealltermsmtcfilt": [1, 2, 35], "user": [15, 19, 21, 23, 26, 30, 31, 34], "usual": [6, 15, 26, 31, 41], "utf": [17, 18], "util": [0, 6, 26], "utr": [15, 34], "uvea": 31, "v": [21, 25, 27, 28, 35], "v2024": [23, 26, 27, 28, 30, 34, 35, 37, 40], "vagin": 31, "val": 2, "val153serfster21": 23, "val214glyfster12": 23, "val263met": [23, 30], "val267trpfster127": [23, 30], "valid": [17, 19, 23, 30, 35], "validation_polici": 17, "validation_runn": 17, "validationrunn": 17, "valu": [1, 2, 3, 4, 8, 9, 10, 12, 15, 16, 17, 19, 23, 24, 26, 27, 28, 33, 35], "valueerror": [5, 15, 16, 17], "valv": 31, "varcachingfunctionalannot": [0, 17], "vari": [6, 26], "variabl": [4, 7, 8, 13, 15, 26, 30, 39], "variable_nam": [7, 8], "variant": [0, 1, 3, 4, 6, 15, 17, 19, 21, 25, 26, 27, 28, 32, 33, 35, 36, 39, 41], "variant_class": [6, 15, 45], "variant_coordin": [15, 17], "variant_effect": [6, 15, 19, 23, 25, 26, 27, 44, 45], "variant_effect_count_by_tx": 15, "variant_fallback": 17, "variant_info": 15, "variant_kei": [6, 15, 17], "variant_key_of_interest": 45, "variant_loc": 19, "variant_locations_counted_absolut": 19, "variantannotationcach": [0, 17], "variantclass": [0, 6, 15, 45], "variantcoordin": [0, 15, 17, 32], "variantcoordinatefind": [0, 17], "varianteffect": [0, 6, 15, 17, 19, 23, 25, 26, 27, 44, 45], "variantformatt": [0, 19], "variantinfo": [0, 15], "variantinfoawar": [0, 15], "variantpred": [5, 6, 23, 25, 26, 27, 28, 36, 39, 41, 44, 45], "varianttranscriptproteinartist": 19, "varianttranscriptvisu": [0, 19], "variou": [16, 37], "vascular": 31, "vasculatur": 31, "vc": [15, 17], "vcf": 15, "vcv000522858": 45, "ventricular": [23, 26, 30, 31, 32], "vep": 17, "vepfunctionalannot": [0, 17], "veri": [2, 44], "verify_term_id": 2, "version": [4, 23, 26, 27, 37, 40], "versu": 28, "vessel": 31, "via": [7, 14, 17, 19, 34], "view": [0, 21, 23, 26, 30, 34], "viewer": [23, 30], "virtual": 22, "vision": 31, "visual": [19, 23, 27, 30, 31, 34], "vital": [11, 15, 23, 30], "vital_statu": 15, "vitalstatu": [0, 15], "vitamin": 31, "voic": 31, "vol": 15, "volum": [8, 15, 25, 27, 31], "vri": [8, 33, 42], "vvhgvsvariantcoordinatefind": [0, 17], "vvmulticoordinateservic": [0, 17, 23, 30, 34], "w": [15, 17], "wa": [1, 2, 3, 5, 7, 15, 19, 23, 25, 26, 27, 28, 30, 35, 37, 40, 45], "wai": [23, 24, 30, 34], "waist": 31, "wall": 31, "want": [2, 8, 26, 27, 34, 35, 36, 44, 45], "warn": [17, 23, 34], "we": [2, 3, 6, 8, 11, 15, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45], "websit": 34, "week": 15, "weight": 31, "well": [6, 7, 15, 30, 34, 38], "were": [1, 3, 17, 19, 23, 26, 27, 30, 34, 40], "what": [26, 39], "whatsoev": 6, "when": [2, 7, 15, 28, 34, 35, 40], "where": [1, 2, 3, 15, 17, 23, 37, 44], "wherea": 30, "whether": [7, 8, 15, 21, 26, 30], "which": [1, 2, 4, 5, 7, 15, 23, 26, 30, 33, 34, 37, 44, 45], "while": [4, 15, 26, 29, 36, 41, 44], "whisker": 27, "whitnei": [8, 9, 24, 30, 33, 37, 42], "who": [7, 23, 27, 29, 44], "whose": [15, 23, 26, 27, 40], "why": 2, "widespread": 30, "wikipedia": 30, "wilcoxon": 27, "wise": [23, 35], "with_cache_fold": 17, "with_strand": 16, "within": [15, 23, 26, 27, 30], "without": [6, 11, 26, 30], "word": [21, 31], "wordsmith": 25, "work": [2, 13, 17, 26, 34], "workflow": 30, "worth": 2, "would": [2, 8, 15, 21, 26, 27, 29, 30, 35, 37, 45], "wrap": [8, 15, 26, 34, 45], "wrap_scoring_funct": 8, "wrapper": [4, 9, 12, 18], "write": [17, 18, 19], "written": 19, "wwox": 40, "x": [27, 28], "x_1000001_1000027_": 15, "x_1000001_1000027_taaaaaaaaaaaaaaaaaaaaaaaaaa_t": 15, "x_12345_12345_c_g": [6, 15], "xaxi": 28, "xlabel": 28, "xm_": 17, "xu": 25, "y": [15, 27, 28], "ye": [1, 3, 7, 40], "year": [15, 17, 28], "yet": 15, "yield": 35, "ylabel": [27, 28], "ylim": 27, "you": [14, 15, 16, 30, 34, 35], "your": [16, 22, 34], "zero": [2, 6, 16, 32, 36, 37], "zero_vs_on": 6, "zero_vs_one_vs_two": 6, "zinc": 15, "zinc_fing": 15, "\u03b1": 15, "\u03c72": 4}, "titles": ["gpsea package", "gpsea.analysis package", "gpsea.analysis.mtc_filter package", "gpsea.analysis.pcats package", "gpsea.analysis.pcats.stats package", "gpsea.analysis.predicate package", "gpsea.analysis.predicate.genotype package", "gpsea.analysis.predicate.phenotype package", "gpsea.analysis.pscore package", "gpsea.analysis.pscore.stats package", "gpsea.analysis.temporal package", "gpsea.analysis.temporal.endpoint package", "gpsea.analysis.temporal.stats package", "gpsea.config module", "gpsea.io module", "gpsea.model package", "gpsea.model.genome package", "gpsea.preprocessing package", "gpsea.util module", "gpsea.view package", "API reference", "GPSEA", "Installation", "Tutorial", "Statistical analyses", "Compare measurement values", "Compare genotype and phenotype groups", "Compare phenotype scores in genotype groups", "Survival analysis", "Genotype-Phenotype Correlations in Autosomal Recessive Diseases", "Cohort exploratory analysis", "General HPO terms", "Glossary", "User guide", "Input data", "Multiple-testing correction", "Group by allele count", "De Vries Score", "Group by diagnosis", "Genotype Predicates", "HPO predicate", "Predicates", "Phenotype Predicates", "Group by sex", "Group by variant category", "Variant Predicates"], "titleterms": {"2x2": 35, "2x3": 35, "The": [23, 37], "abnorm": [35, 37], "across": 30, "all": [23, 35, 40], "allel": [23, 32, 36], "altern": 34, "an": 32, "analys": 24, "analysi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 25, 26, 27, 28, 30, 35], "api": [20, 34], "ar": 35, "associ": 26, "autosom": 29, "background": 35, "biallel": [36, 44], "block": 45, "build": 45, "categori": 44, "chang": 32, "child": 35, "choos": [34, 35], "code": 37, "cohort": [23, 25, 26, 27, 28, 30, 34, 35, 40, 45], "compar": [25, 26, 27, 36], "complex": 45, "condit": 45, "config": 13, "configur": [25, 26, 27, 28, 34], "congenit": 37, "content": [24, 33, 39, 41, 42], "control": 34, "coordin": 34, "correct": 35, "correl": 29, "count": [35, 36], "creat": 34, "creator": 34, "curv": 28, "custom": 26, "data": [28, 34], "de": 37, "default": 26, "delai": 37, "descend": 35, "development": 37, "diagnosi": 38, "diseas": 29, "distribut": [23, 30, 34], "domain": 30, "dump": 34, "dysmorph": 37, "egfr": 36, "endpoint": [11, 28], "enter": 34, "exact": 26, "exampl": [25, 26, 27, 28, 34, 36, 40, 44], "exclud": 35, "explor": [23, 30], "exploratori": 30, "facial": 37, "featur": [34, 37], "feedback": 21, "fet": 26, "fetch": 34, "filter": 35, "final": [25, 27, 28, 37], "fisher": 26, "frameshift": [23, 26], "from": 34, "ga4gh": 34, "galleri": 41, "gener": [31, 35], "genom": 16, "genotyp": [6, 23, 25, 26, 27, 28, 29, 34, 35, 39, 44], "get": 34, "glossari": 32, "gpsea": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 35], "group": [26, 27, 35, 36, 38, 43, 44], "growth": 37, "guid": 33, "ha": 35, "hmf01": 35, "hmf02": 35, "hmf03": 35, "hmf05": 35, "hmf06": 35, "hmf07": 35, "hmf08": 35, "hmf09": 35, "hpo": [23, 27, 31, 35, 40], "ident": 35, "implement": 35, "individu": 36, "input": 34, "instal": 22, "interact": 30, "interest": 34, "invert": 45, "io": 14, "json": 34, "kaplan": 28, "later": 34, "latest": 22, "length": 32, "level": 35, "literatur": 21, "load": [23, 25, 26, 27, 28, 34, 45], "mann": 27, "manual": 34, "measur": 25, "meier": 28, "missens": 23, "missing_implies_phenotype_exclud": 40, "model": [15, 16], "modul": [13, 14, 18], "monoallel": [36, 44], "more": [35, 41], "mt": 35, "mtc_filter": 2, "multipl": 35, "mutat": 36, "need": 41, "neither": 35, "non": 37, "nor": 35, "observ": 35, "occur": 35, "one": 35, "onset": 37, "packag": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19], "pars": 34, "partit": 44, "path": 32, "pcat": [3, 4], "persist": 34, "phenopacket": 34, "phenotyp": [7, 23, 25, 26, 27, 29, 34, 35, 40, 42], "plot": [23, 30, 34], "postnat": 37, "power": 30, "predic": [5, 6, 7, 23, 25, 26, 27, 28, 39, 40, 41, 42, 44, 45], "prenat": 37, "prepar": 23, "preprocess": 17, "procedur": 35, "protein": [23, 30, 34], "provid": 34, "pscore": [8, 9], "qualiti": 34, "rare": 35, "raw": 28, "recess": 29, "refer": [20, 32], "releas": 22, "respect": [23, 30], "rest": [26, 34], "retard": 37, "rule": 32, "run": 22, "score": [25, 27, 37], "scorer": 37, "section": 37, "sequenc": [23, 30], "sex": 43, "shape": 4, "show": 23, "showcas": 34, "skip": 35, "sourc": 34, "specifi": 35, "stabl": 22, "standard": 34, "stat": [4, 9, 12], "statist": [24, 25, 26, 27, 28, 30], "strategi": 35, "submodul": 0, "subpackag": [0, 1, 3, 5, 8, 10, 15], "summar": 23, "summari": [23, 30], "support": 4, "surviv": 28, "tbx5": [23, 26], "tempor": [10, 11, 12], "term": [31, 35], "test": [22, 25, 26, 27, 28, 30, 35], "than": 35, "transcript": 34, "true": 32, "tutori": [23, 29], "type": 30, "u": 27, "underpow": 35, "uniprot": 34, "us": 37, "user": 33, "util": 18, "v": [23, 26], "valid": 34, "valu": 25, "variant": [23, 30, 34, 44, 45], "veri": 35, "view": 19, "vri": 37, "which": 35, "whitnei": 27}})
\ No newline at end of file