GPSEA
0.4
Installation & Tutorial
Installation
Tutorial
User guide
API reference
GPSEA
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Y
A
add_error() (gpsea.preprocessing.Notepad method)
add_issue() (gpsea.preprocessing.Notepad method)
add_subsection() (gpsea.preprocessing.Notepad method)
(gpsea.preprocessing.NotepadTree method)
add_warning() (gpsea.preprocessing.Notepad method)
all() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
all_counts (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property)
all_diseases() (gpsea.model.Cohort method)
all_patients (gpsea.model.Cohort property)
all_phenotypes() (gpsea.model.Cohort method)
all_transcript_ids (gpsea.model.Cohort property)
all_variants() (gpsea.model.Cohort method)
AlleleCounter (class in gpsea.analysis.predicate.genotype)
alt (gpsea.model.VariantCoordinates property)
annotate() (gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator method)
(gpsea.preprocessing.FunctionalAnnotator method)
(gpsea.preprocessing.ImpreciseSvFunctionalAnnotator method)
(gpsea.preprocessing.ProtCachingMetadataService method)
(gpsea.preprocessing.ProteinMetadataService method)
(gpsea.preprocessing.UniprotProteinMetadataService method)
(gpsea.preprocessing.VarCachingFunctionalAnnotator method)
(gpsea.preprocessing.VepFunctionalAnnotator method)
any() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
apply_predicates_on_patients() (in module gpsea.analysis.pcats)
Auditor (class in gpsea.preprocessing)
autosomal_dominant() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)
(in module gpsea.analysis.predicate.genotype)
autosomal_recessive() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate static method)
(in module gpsea.analysis.predicate.genotype)
B
biallelic_predicate() (in module gpsea.analysis.predicate.genotype)
BND (gpsea.model.VariantClass attribute)
C
CACHE_ENV (in module gpsea.config)
cat_id (gpsea.analysis.predicate.PatientCategory property)
Categorization (class in gpsea.analysis.predicate)
category (gpsea.analysis.predicate.Categorization property)
cds_end (gpsea.model.TranscriptCoordinates property)
cds_start (gpsea.model.TranscriptCoordinates property)
change_length (gpsea.model.VariantCoordinates property)
change_length() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
children (gpsea.preprocessing.NotepadTree property)
chrom (gpsea.model.VariantCoordinates property)
code (gpsea.analysis.mtc_filter.PhenotypeMtcIssue attribute)
(gpsea.model.Genotype property)
CODING_SEQUENCE_VARIANT (gpsea.model.VariantEffect attribute)
Cohort (class in gpsea.model)
CohortCreator (class in gpsea.preprocessing)
CohortVariantViewer (class in gpsea.view)
CohortViewable (class in gpsea.view)
compare_genotype_vs_phenotype_score() (gpsea.analysis.pscore.PhenotypeScoreAnalysis method)
compare_genotype_vs_phenotypes() (gpsea.analysis.pcats.MultiPhenotypeAnalysis method)
compute_pval() (gpsea.analysis.pcats.stats.CountStatistic method)
(gpsea.analysis.pcats.stats.FisherExactTest method)
(gpsea.analysis.pscore.stats.MannWhitneyStatistic method)
(gpsea.analysis.pscore.stats.PhenotypeScoreStatistic method)
(gpsea.analysis.pscore.stats.TTestStatistic method)
configure_caching_cohort_creator() (in module gpsea.preprocessing)
configure_caching_patient_creator() (in module gpsea.preprocessing)
configure_cohort_creator() (in module gpsea.preprocessing)
configure_default_protein_metadata_service() (in module gpsea.preprocessing)
configure_patient_creator() (in module gpsea.preprocessing)
configure_protein_metadata_service() (in module gpsea.preprocessing)
contains() (gpsea.model.genome.GenomicRegion method)
(gpsea.model.genome.Region method)
contains_pos() (gpsea.model.genome.Region method)
Contig (class in gpsea.model.genome)
contig (gpsea.model.genome.GenomicRegion property)
contig_by_name() (gpsea.model.genome.GenomeBuild method)
contigs (gpsea.model.genome.GenomeBuild property)
corrected_pvals (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property)
count() (gpsea.analysis.predicate.genotype.AlleleCounter method)
CountingPhenotypeScorer (class in gpsea.analysis.pscore)
CountStatistic (class in gpsea.analysis.pcats.stats)
create() (gpsea.model.ProteinFeature static method)
create_variant_from_scratch() (gpsea.model.Variant static method)
curie (gpsea.model.VariantEffect property)
D
DataSanityIssue (class in gpsea.preprocessing)
default() (gpsea.io.GpseaJSONEncoder method)
DEFAULT_CACHE_PATH (in module gpsea.config)
default_filter() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)
DefaultImpreciseSvFunctionalAnnotator (class in gpsea.preprocessing)
DEL (gpsea.model.VariantClass attribute)
description (gpsea.analysis.predicate.PatientCategory property)
DeVriesPhenotypeScorer (class in gpsea.analysis.pscore)
diagnosis_predicate() (in module gpsea.analysis.predicate.genotype)
Disease (class in gpsea.model)
DiseaseAnalysis (class in gpsea.analysis.pcats)
DiseasePresencePredicate (class in gpsea.analysis.predicate.phenotype)
diseases (gpsea.model.Patient property)
DiseaseViewable (class in gpsea.view)
display_question() (gpsea.analysis.predicate.PolyPredicate method)
distance_to() (gpsea.model.genome.GenomicRegion method)
(gpsea.model.genome.Region method)
DOMAIN (gpsea.model.FeatureType attribute)
domains() (gpsea.model.ProteinMetadata method)
DOWNSTREAM_GENE_VARIANT (gpsea.model.VariantEffect attribute)
draw_fig() (gpsea.view.ProteinVisualizer method)
draw_protein_diagram() (gpsea.view.ProteinVisualizer method)
draw_variants() (gpsea.view.VariantTranscriptVisualizer method)
DUP (gpsea.model.VariantClass attribute)
E
empty() (gpsea.model.Genotypes static method)
end (gpsea.model.FeatureInfo property)
(gpsea.model.genome.Region property)
(gpsea.model.VariantCoordinates property)
end_on_strand() (gpsea.model.genome.GenomicRegion method)
ERROR (gpsea.preprocessing.Level attribute)
error_count() (gpsea.preprocessing.Notepad method)
errors() (gpsea.preprocessing.Notepad method)
excluded_diseases() (gpsea.model.Patient method)
excluded_phenotypes() (gpsea.model.Patient method)
exon() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
exons (gpsea.model.TranscriptCoordinates property)
F
fail() (gpsea.analysis.mtc_filter.PhenotypeMtcResult static method)
FEATURE_ELONGATION (gpsea.model.VariantEffect attribute)
FEATURE_TRUNCATION (gpsea.model.VariantEffect attribute)
feature_type (gpsea.model.ProteinFeature property)
FeatureInfo (class in gpsea.model)
FeatureType (class in gpsea.model)
FEMALE (gpsea.model.Sex attribute)
fetch() (gpsea.preprocessing.TranscriptCoordinateService method)
(gpsea.preprocessing.VVMultiCoordinateService method)
fetch_for_gene() (gpsea.preprocessing.GeneCoordinateService method)
(gpsea.preprocessing.VVMultiCoordinateService method)
fetch_response() (gpsea.preprocessing.VepFunctionalAnnotator method)
filter() (gpsea.analysis.mtc_filter.HpoMtcFilter method)
(gpsea.analysis.mtc_filter.PhenotypeMtcFilter method)
(gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter method)
(gpsea.analysis.mtc_filter.UseAllTermsMtcFilter method)
filter_method_name() (gpsea.analysis.mtc_filter.HpoMtcFilter method)
(gpsea.analysis.mtc_filter.PhenotypeMtcFilter method)
(gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter method)
(gpsea.analysis.mtc_filter.UseAllTermsMtcFilter method)
find_coordinates() (gpsea.preprocessing.PhenopacketVariantCoordinateFinder method)
(gpsea.preprocessing.VariantCoordinateFinder method)
(gpsea.preprocessing.VVHgvsVariantCoordinateFinder method)
FisherExactTest (class in gpsea.analysis.pcats.stats)
FIVE_PRIME_UTR_VARIANT (gpsea.model.VariantEffect attribute)
for_sample() (gpsea.model.Genotypes method)
format_as_string() (gpsea.view.VariantFormatter method)
format_coordinates_for_vep_query() (gpsea.preprocessing.VepFunctionalAnnotator static method)
FRAMESHIFT_VARIANT (gpsea.model.VariantEffect attribute)
from_mapping() (gpsea.model.Genotypes static method)
from_patients() (gpsea.model.Cohort static method)
from_query_curies() (gpsea.analysis.pscore.CountingPhenotypeScorer static method)
from_raw_parts() (gpsea.analysis.predicate.Categorization static method)
(gpsea.model.Patient static method)
(gpsea.model.Phenotype static method)
from_term() (gpsea.model.Phenotype static method)
from_vcf_literal() (gpsea.model.VariantCoordinates static method)
from_vcf_symbolic() (gpsea.model.VariantCoordinates static method)
FunctionalAnnotator (class in gpsea.preprocessing)
G
genbank_acc (gpsea.model.genome.Contig property)
gene() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
gene_id (gpsea.model.ImpreciseSvInfo property)
(gpsea.model.TranscriptAnnotation property)
(gpsea.model.TranscriptInfoAware property)
gene_symbol (gpsea.model.ImpreciseSvInfo property)
GeneCoordinateService (class in gpsea.preprocessing)
genome_build_id (gpsea.model.genome.GenomeBuild property)
GenomeBuild (class in gpsea.model.genome)
GenomeBuildIdentifier (class in gpsea.model.genome)
GenomicRegion (class in gpsea.model.genome)
Genotype (class in gpsea.model)
genotype_for_sample() (gpsea.model.Genotyped method)
genotype_phenotype_scores (gpsea.analysis.pscore.PhenotypeScoreAnalysisResult property)
Genotyped (class in gpsea.model)
GenotypePolyPredicate (class in gpsea.analysis.predicate.genotype)
Genotypes (class in gpsea.model)
genotypes (gpsea.model.Genotyped property)
(gpsea.model.Variant property)
genotypes_have_same_hpo_proportions() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)
get_annotations() (gpsea.preprocessing.ProteinAnnotationCache method)
(gpsea.preprocessing.VariantAnnotationCache method)
get_cache_dir_path() (in module gpsea.config)
get_categories() (gpsea.analysis.predicate.PolyPredicate method)
get_categorizations() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate method)
(gpsea.analysis.predicate.phenotype.DiseasePresencePredicate method)
(gpsea.analysis.predicate.phenotype.HpoPredicate method)
(gpsea.analysis.predicate.PolyPredicate method)
get_category() (gpsea.analysis.predicate.PolyPredicate method)
get_category_name() (gpsea.analysis.predicate.PolyPredicate method)
get_category_names() (gpsea.analysis.predicate.PolyPredicate method)
get_cds_regions() (gpsea.model.TranscriptCoordinates method)
get_coding_base_count() (gpsea.model.TranscriptCoordinates method)
get_codon_count() (gpsea.model.TranscriptCoordinates method)
get_excluded_count() (gpsea.model.Cohort method)
get_features_variant_overlaps() (gpsea.model.ProteinMetadata method)
get_five_prime_utrs() (gpsea.model.TranscriptCoordinates method)
get_maximum_group_observed_HPO_frequency() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)
get_number_of_observed_hpo_observations() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)
get_patient_ids() (gpsea.model.Cohort method)
get_question() (gpsea.analysis.predicate.genotype.AlleleCounter method)
(gpsea.analysis.predicate.genotype.VariantPredicate method)
(gpsea.analysis.pscore.CountingPhenotypeScorer method)
get_question_base() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate method)
(gpsea.analysis.predicate.phenotype.DiseasePresencePredicate method)
(gpsea.analysis.predicate.phenotype.HpoPredicate method)
(gpsea.analysis.predicate.PolyPredicate method)
get_response() (gpsea.preprocessing.VVMultiCoordinateService method)
get_three_prime_utrs() (gpsea.model.TranscriptCoordinates method)
get_variant_by_key() (gpsea.model.Cohort method)
gpsea
module
gpsea.analysis
module
gpsea.analysis.mtc_filter
module
gpsea.analysis.pcats
module
gpsea.analysis.pcats.stats
module
gpsea.analysis.predicate
module
gpsea.analysis.predicate.genotype
module
gpsea.analysis.predicate.phenotype
module
gpsea.analysis.pscore
module
gpsea.analysis.pscore.stats
module
gpsea.config
module
gpsea.io
module
gpsea.model
module
gpsea.model.genome
module
gpsea.preprocessing
module
gpsea.view
module
GpseaJSONDecoder (class in gpsea.io)
GpseaJSONEncoder (class in gpsea.io)
groups_predicate() (in module gpsea.analysis.predicate.genotype)
H
has_errors() (gpsea.preprocessing.NotepadTree method)
has_errors_or_warnings() (gpsea.preprocessing.NotepadTree method)
has_sv_info() (gpsea.model.VariantInfo method)
has_variant_coordinates() (gpsea.model.VariantInfo method)
has_warnings() (gpsea.preprocessing.NotepadTree method)
HEMIZYGOUS (gpsea.model.Genotype attribute)
HETEROZYGOUS (gpsea.model.Genotype attribute)
hgvs_cdna (gpsea.model.TranscriptAnnotation property)
hgvsp (gpsea.model.TranscriptAnnotation property)
HOMOZYGOUS_ALTERNATE (gpsea.model.Genotype attribute)
HOMOZYGOUS_REFERENCE (gpsea.model.Genotype attribute)
HpoMtcFilter (class in gpsea.analysis.mtc_filter)
HpoPredicate (class in gpsea.analysis.predicate.phenotype)
HpoTermAnalysis (class in gpsea.analysis.pcats)
HpoTermAnalysisResult (class in gpsea.analysis.pcats)
I
identifier (gpsea.model.Disease property)
(gpsea.model.genome.GenomeBuild property)
(gpsea.model.genome.GenomeBuildIdentifier property)
(gpsea.model.Phenotype property)
(gpsea.model.TranscriptCoordinates property)
ImpreciseSvFunctionalAnnotator (class in gpsea.preprocessing)
ImpreciseSvInfo (class in gpsea.model)
INCOMPLETE_TERMINAL_CODON_VARIANT (gpsea.model.VariantEffect attribute)
info (gpsea.model.ProteinFeature property)
INFRAME_DELETION (gpsea.model.VariantEffect attribute)
INFRAME_INSERTION (gpsea.model.VariantEffect attribute)
INS (gpsea.model.VariantClass attribute)
INTERGENIC_VARIANT (gpsea.model.VariantEffect attribute)
INTRON_VARIANT (gpsea.model.VariantEffect attribute)
INV (gpsea.model.VariantClass attribute)
is_coding() (gpsea.model.TranscriptCoordinates method)
is_empty() (gpsea.model.genome.Region method)
is_female() (gpsea.model.Sex method)
is_filtered_out() (gpsea.analysis.mtc_filter.PhenotypeMtcResult method)
is_large_imprecise_sv() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
is_male() (gpsea.model.Sex method)
is_negative() (gpsea.model.genome.Strand method)
is_observed (gpsea.model.Phenotype property)
is_passed() (gpsea.analysis.mtc_filter.PhenotypeMtcResult method)
is_positive() (gpsea.model.genome.Strand method)
is_preferred (gpsea.model.TranscriptAnnotation property)
(gpsea.model.TranscriptCoordinates property)
is_present (gpsea.model.Disease property)
(gpsea.model.Phenotype property)
is_provided() (gpsea.model.Sex method)
is_structural() (gpsea.model.VariantCoordinates method)
(gpsea.model.VariantInfo method)
is_structural_deletion() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
is_structural_variant() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
is_unknown() (gpsea.model.Sex method)
issues (gpsea.preprocessing.Notepad property)
iterate_nodes() (gpsea.preprocessing.NotepadTree method)
L
label (gpsea.model.ProteinMetadata property)
(gpsea.model.SampleLabels property)
(gpsea.preprocessing.Notepad property)
label_summary() (gpsea.model.SampleLabels method)
labels (gpsea.model.Patient property)
Level (class in gpsea.preprocessing)
level (gpsea.preprocessing.DataSanityIssue property)
(gpsea.preprocessing.NotepadTree property)
list_all_diseases() (gpsea.model.Cohort method)
list_all_proteins() (gpsea.model.Cohort method)
list_all_variants() (gpsea.model.Cohort method)
list_present_phenotypes() (gpsea.model.Cohort method)
load_phenopacket_files() (in module gpsea.preprocessing)
load_phenopacket_folder() (in module gpsea.preprocessing)
load_phenopackets() (in module gpsea.preprocessing)
M
major_assembly (gpsea.model.genome.GenomeBuildIdentifier property)
MALE (gpsea.model.Sex attribute)
MannWhitneyStatistic (class in gpsea.analysis.pscore.stats)
marker_counts (gpsea.view.ProteinVisualizable property)
MATURE_MIRNA_VARIANT (gpsea.model.VariantEffect attribute)
message (gpsea.preprocessing.DataSanityIssue property)
meta_label (gpsea.model.SampleLabels property)
MISSENSE_VARIANT (gpsea.model.VariantEffect attribute)
MNV (gpsea.model.VariantClass attribute)
ModeOfInheritancePredicate (class in gpsea.analysis.predicate.genotype)
module
gpsea
gpsea.analysis
gpsea.analysis.mtc_filter
gpsea.analysis.pcats
gpsea.analysis.pcats.stats
gpsea.analysis.predicate
gpsea.analysis.predicate.genotype
gpsea.analysis.predicate.phenotype
gpsea.analysis.pscore
gpsea.analysis.pscore.stats
gpsea.config
gpsea.io
gpsea.model
gpsea.model.genome
gpsea.preprocessing
gpsea.view
monoallelic_predicate() (in module gpsea.analysis.predicate.genotype)
MOTIF (gpsea.model.FeatureType attribute)
motifs() (gpsea.model.ProteinMetadata method)
mtc_filter_name (gpsea.analysis.pcats.HpoTermAnalysisResult property)
mtc_filter_results (gpsea.analysis.pcats.HpoTermAnalysisResult property)
mtc_issue (gpsea.analysis.mtc_filter.PhenotypeMtcResult property)
mtc_name (gpsea.analysis.pcats.HpoTermAnalysisResult property)
MtcStatsViewer (class in gpsea.view)
MultiPhenotypeAnalysis (class in gpsea.analysis.pcats)
MultiPhenotypeAnalysisResult (class in gpsea.analysis.pcats)
N
n_categorizations() (gpsea.analysis.predicate.PolyPredicate method)
n_usable (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property)
name (gpsea.analysis.predicate.PatientCategory property)
(gpsea.model.Disease property)
(gpsea.model.FeatureInfo property)
(gpsea.model.genome.Contig property)
NEGATIVE (gpsea.model.genome.Strand attribute)
NMD_TRANSCRIPT_VARIANT (gpsea.model.VariantEffect attribute)
NO (gpsea.analysis.predicate.PatientCategories attribute)
NO_CALL (gpsea.model.Genotype attribute)
NO_GENOTYPE_HAS_MORE_THAN_ONE_HPO (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)
NON_CODING_TRANSCRIPT_EXON_VARIANT (gpsea.model.VariantEffect attribute)
NON_CODING_TRANSCRIPT_VARIANT (gpsea.model.VariantEffect attribute)
NON_SPECIFIED_TERM (gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter attribute)
NONCODING_EFFECTS (gpsea.preprocessing.VepFunctionalAnnotator attribute)
Notepad (class in gpsea.preprocessing)
NotepadTree (class in gpsea.preprocessing)
O
object_hook() (gpsea.io.GpseaJSONDecoder static method)
observed (gpsea.model.Phenotype property)
OK (gpsea.analysis.mtc_filter.PhenotypeMtcFilter attribute)
ok() (gpsea.analysis.mtc_filter.PhenotypeMtcResult static method)
one_genotype_has_zero_hpo_observations() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)
opposite() (gpsea.model.genome.Strand method)
overlapping_exons (gpsea.model.TranscriptAnnotation property)
overlaps_with() (gpsea.model.genome.GenomicRegion method)
(gpsea.model.genome.Region method)
P
parse_multiple() (gpsea.preprocessing.VVMultiCoordinateService method)
parse_response() (gpsea.preprocessing.VVMultiCoordinateService method)
parse_uniprot_json() (gpsea.preprocessing.UniprotProteinMetadataService static method)
patch (gpsea.model.genome.GenomeBuildIdentifier property)
Patient (class in gpsea.model)
patient_id (gpsea.model.Patient property)
PatientCategories (class in gpsea.analysis.predicate)
PatientCategory (class in gpsea.analysis.predicate)
PatientCreator (class in gpsea.preprocessing)
PhenopacketPatientCreator (class in gpsea.preprocessing)
PhenopacketVariantCoordinateFinder (class in gpsea.preprocessing)
Phenotype (class in gpsea.model)
phenotype (gpsea.analysis.predicate.phenotype.DiseasePresencePredicate property)
(gpsea.analysis.predicate.phenotype.HpoPredicate property)
(gpsea.analysis.predicate.phenotype.PhenotypeCategorization property)
(gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate property)
PhenotypeCategorization (class in gpsea.analysis.predicate.phenotype)
PhenotypeCreator (class in gpsea.preprocessing)
PhenotypeMtcFilter (class in gpsea.analysis.mtc_filter)
PhenotypeMtcIssue (class in gpsea.analysis.mtc_filter)
PhenotypeMtcResult (class in gpsea.analysis.mtc_filter)
PhenotypePolyPredicate (class in gpsea.analysis.predicate.phenotype)
phenotypes (gpsea.model.Patient property)
PhenotypeScoreAnalysis (class in gpsea.analysis.pscore)
PhenotypeScoreAnalysisResult (class in gpsea.analysis.pscore)
PhenotypeScorer (class in gpsea.analysis.pscore)
PhenotypeScoreStatistic (class in gpsea.analysis.pscore.stats)
plot_boxplots() (gpsea.analysis.pscore.PhenotypeScoreAnalysisResult method)
PolyPredicate (class in gpsea.analysis.predicate)
POSITIVE (gpsea.model.genome.Strand attribute)
possible_results() (gpsea.analysis.mtc_filter.HpoMtcFilter method)
(gpsea.analysis.mtc_filter.PhenotypeMtcFilter method)
(gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter method)
(gpsea.analysis.mtc_filter.UseAllTermsMtcFilter method)
prepare_hpo_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)
prepare_notepad() (gpsea.preprocessing.Auditor static method)
prepare_predicates_for_terms_of_interest() (in module gpsea.analysis.predicate.phenotype)
present_diseases() (gpsea.model.Patient method)
present_phenotype_categorization (gpsea.analysis.predicate.phenotype.DiseasePresencePredicate property)
(gpsea.analysis.predicate.phenotype.HpoPredicate property)
(gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate property)
present_phenotype_category (gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate property)
present_phenotypes() (gpsea.model.Patient method)
process() (gpsea.preprocessing.Auditor method)
(gpsea.preprocessing.CohortCreator method)
(gpsea.preprocessing.PhenopacketPatientCreator method)
(gpsea.preprocessing.PhenotypeCreator method)
(gpsea.view.CohortVariantViewer method)
(gpsea.view.CohortViewable method)
(gpsea.view.DiseaseViewable method)
(gpsea.view.MtcStatsViewer method)
(gpsea.view.ProteinViewable method)
process_response() (gpsea.preprocessing.VepFunctionalAnnotator method)
ProtCachingMetadataService (class in gpsea.preprocessing)
PROTEIN_ALTERING_VARIANT (gpsea.model.VariantEffect attribute)
protein_effect_location (gpsea.model.TranscriptAnnotation property)
protein_feature() (gpsea.analysis.predicate.genotype.ProteinPredicates method)
protein_feature_ends (gpsea.view.ProteinVisualizable property)
protein_feature_names (gpsea.view.ProteinVisualizable property)
protein_feature_starts (gpsea.view.ProteinVisualizable property)
protein_feature_type() (gpsea.analysis.predicate.genotype.ProteinPredicates method)
protein_feature_types (gpsea.view.ProteinVisualizable property)
protein_features (gpsea.model.ProteinMetadata property)
protein_id (gpsea.model.ProteinMetadata property)
(gpsea.model.TranscriptAnnotation property)
(gpsea.view.ProteinVisualizable property)
protein_length (gpsea.model.ProteinMetadata property)
(gpsea.view.ProteinVisualizable property)
protein_metadata (gpsea.view.ProteinVisualizable property)
ProteinAnnotationCache (class in gpsea.preprocessing)
ProteinFeature (class in gpsea.model)
ProteinMetadata (class in gpsea.model)
ProteinMetadataService (class in gpsea.preprocessing)
ProteinPredicates (class in gpsea.analysis.predicate.genotype)
ProteinViewable (class in gpsea.view)
ProteinVisualizable (class in gpsea.view)
ProteinVisualizer (class in gpsea.view)
pval (gpsea.analysis.pscore.PhenotypeScoreAnalysisResult property)
pvals (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property)
R
reason (gpsea.analysis.mtc_filter.PhenotypeMtcIssue attribute)
(gpsea.analysis.mtc_filter.PhenotypeMtcResult property)
ref (gpsea.model.VariantCoordinates property)
ref_length() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
refseq_name (gpsea.model.genome.Contig property)
Region (class in gpsea.model.genome)
region (gpsea.model.FeatureInfo property)
REGION (gpsea.model.FeatureType attribute)
region (gpsea.model.TranscriptCoordinates property)
(gpsea.model.VariantCoordinates property)
region() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
regions() (gpsea.model.ProteinMetadata method)
REGULATORY_REGION_ABLATION (gpsea.model.VariantEffect attribute)
REGULATORY_REGION_AMPLIFICATION (gpsea.model.VariantEffect attribute)
REGULATORY_REGION_VARIANT (gpsea.model.VariantEffect attribute)
REPEAT (gpsea.model.FeatureType attribute)
repeats() (gpsea.model.ProteinMetadata method)
S
SAME_COUNT_AS_THE_ONLY_CHILD (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)
SampleLabels (class in gpsea.model)
score() (gpsea.analysis.pscore.CountingPhenotypeScorer method)
(gpsea.analysis.pscore.DeVriesPhenotypeScorer method)
(gpsea.analysis.pscore.PhenotypeScorer method)
SEQUENCE_VARIANT (gpsea.model.VariantEffect attribute)
Sex (class in gpsea.model)
sex (gpsea.model.Patient property)
sex_predicate() (in module gpsea.analysis.predicate.genotype)
single() (gpsea.model.Genotypes static method)
SKIPPING_GENERAL_TERM (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)
SKIPPING_NON_PHENOTYPE_TERM (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)
SKIPPING_SAME_OBSERVED_PROPORTIONS (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)
SKIPPING_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS (gpsea.analysis.mtc_filter.HpoMtcFilter attribute)
SNV (gpsea.model.VariantClass attribute)
solution (gpsea.preprocessing.DataSanityIssue property)
some_cell_has_greater_than_one_count() (gpsea.analysis.mtc_filter.HpoMtcFilter static method)
SpecifiedTermsMtcFilter (class in gpsea.analysis.mtc_filter)
SPLICE_ACCEPTOR_VARIANT (gpsea.model.VariantEffect attribute)
SPLICE_DONOR_5TH_BASE_VARIANT (gpsea.model.VariantEffect attribute)
SPLICE_DONOR_REGION_VARIANT (gpsea.model.VariantEffect attribute)
SPLICE_DONOR_VARIANT (gpsea.model.VariantEffect attribute)
SPLICE_POLYPYRIMIDINE_TRACT_VARIANT (gpsea.model.VariantEffect attribute)
SPLICE_REGION_VARIANT (gpsea.model.VariantEffect attribute)
start (gpsea.model.FeatureInfo property)
(gpsea.model.genome.Region property)
(gpsea.model.VariantCoordinates property)
START_LOST (gpsea.model.VariantEffect attribute)
start_on_strand() (gpsea.model.genome.GenomicRegion method)
START_RETAINED_VARIANT (gpsea.model.VariantEffect attribute)
STOP_GAINED (gpsea.model.VariantEffect attribute)
STOP_LOST (gpsea.model.VariantEffect attribute)
STOP_RETAINED_VARIANT (gpsea.model.VariantEffect attribute)
store_annotations() (gpsea.preprocessing.ProteinAnnotationCache method)
(gpsea.preprocessing.VariantAnnotationCache method)
Strand (class in gpsea.model.genome)
strand (gpsea.model.genome.GenomicRegion property)
(gpsea.model.genome.Stranded property)
Stranded (class in gpsea.model.genome)
structural_so_id_to_display() (gpsea.model.VariantEffect static method)
structural_type (gpsea.model.ImpreciseSvInfo property)
structural_type() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
summarize_hpo_analysis() (in module gpsea.view)
supports_shape (gpsea.analysis.pcats.stats.CountStatistic property)
(gpsea.analysis.pcats.stats.FisherExactTest property)
sv_info (gpsea.model.VariantInfo property)
symbol (gpsea.model.genome.Strand property)
SYNONYMOUS_VARIANT (gpsea.model.VariantEffect attribute)
T
test() (gpsea.analysis.predicate.genotype.ModeOfInheritancePredicate method)
(gpsea.analysis.predicate.genotype.VariantPredicate method)
(gpsea.analysis.predicate.phenotype.DiseasePresencePredicate method)
(gpsea.analysis.predicate.phenotype.HpoPredicate method)
(gpsea.analysis.predicate.PolyPredicate method)
TF_BINDING_SITE_VARIANT (gpsea.model.VariantEffect attribute)
TFBS_ABLATION (gpsea.model.VariantEffect attribute)
TFBS_AMPLIFICATION (gpsea.model.VariantEffect attribute)
THREE_PRIME_UTR_VARIANT (gpsea.model.VariantEffect attribute)
to_display() (gpsea.model.VariantEffect method)
to_negative_strand() (gpsea.model.genome.Transposable method)
to_opposite_strand() (gpsea.model.genome.Transposable method)
to_positive_strand() (gpsea.model.genome.Transposable method)
to_string() (gpsea.model.ProteinFeature method)
total_patient_count (gpsea.model.Cohort property)
total_tests (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property)
transcript() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
TRANSCRIPT_ABLATION (gpsea.model.VariantEffect attribute)
TRANSCRIPT_AMPLIFICATION (gpsea.model.VariantEffect attribute)
transcript_coordinates (gpsea.view.ProteinVisualizable property)
transcript_id (gpsea.model.TranscriptAnnotation property)
(gpsea.model.TranscriptInfoAware property)
(gpsea.view.ProteinVisualizable property)
TranscriptAnnotation (class in gpsea.model)
TranscriptCoordinates (class in gpsea.model)
TranscriptCoordinateService (class in gpsea.preprocessing)
TranscriptInfoAware (class in gpsea.model)
Transposable (class in gpsea.model.genome)
transpose_coordinate() (in module gpsea.model.genome)
true() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
TTestStatistic (class in gpsea.analysis.pscore.stats)
tx_annotations (gpsea.model.Variant property)
U
ucsc_name (gpsea.model.genome.Contig property)
UniprotProteinMetadataService (class in gpsea.preprocessing)
UNKNOWN_SEX (gpsea.model.Sex attribute)
UPSTREAM_GENE_VARIANT (gpsea.model.VariantEffect attribute)
UseAllTermsMtcFilter (class in gpsea.analysis.mtc_filter)
V
VarCachingFunctionalAnnotator (class in gpsea.preprocessing)
Variant (class in gpsea.model)
variant_class (gpsea.model.ImpreciseSvInfo property)
(gpsea.model.VariantCoordinates property)
(gpsea.model.VariantInfo property)
variant_class() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
variant_coordinates (gpsea.model.VariantInfo property)
variant_effect() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
variant_effect_count_by_tx() (gpsea.model.Cohort method)
variant_effects (gpsea.model.TranscriptAnnotation property)
(gpsea.view.ProteinVisualizable property)
variant_info (gpsea.model.Variant property)
(gpsea.model.VariantInfoAware property)
variant_key (gpsea.model.ImpreciseSvInfo property)
(gpsea.model.VariantCoordinates property)
(gpsea.model.VariantInfo property)
variant_key() (gpsea.analysis.predicate.genotype.VariantPredicates static method)
variant_locations (gpsea.view.ProteinVisualizable property)
variant_locations_counted_absolute (gpsea.view.ProteinVisualizable property)
VariantAnnotationCache (class in gpsea.preprocessing)
VariantClass (class in gpsea.model)
VariantCoordinateFinder (class in gpsea.preprocessing)
VariantCoordinates (class in gpsea.model)
VariantEffect (class in gpsea.model)
VariantFormatter (class in gpsea.view)
VariantInfo (class in gpsea.model)
VariantInfoAware (class in gpsea.model)
VariantPredicate (class in gpsea.analysis.predicate.genotype)
VariantPredicates (class in gpsea.analysis.predicate.genotype)
variants (gpsea.model.Patient property)
VariantTranscriptVisualizer (class in gpsea.view)
VepFunctionalAnnotator (class in gpsea.preprocessing)
visit() (gpsea.preprocessing.NotepadTree method)
VVHgvsVariantCoordinateFinder (class in gpsea.preprocessing)
VVMultiCoordinateService (class in gpsea.preprocessing)
W
WARN (gpsea.preprocessing.Level attribute)
warning_count() (gpsea.preprocessing.Notepad method)
warnings() (gpsea.preprocessing.Notepad method)
with_cache_folder() (gpsea.preprocessing.VarCachingFunctionalAnnotator static method)
with_strand() (gpsea.model.genome.GenomicRegion method)
(gpsea.model.genome.Transposable method)
wrap_scoring_function() (gpsea.analysis.pscore.PhenotypeScorer static method)
Y
YES (gpsea.analysis.predicate.PatientCategories attribute)