Index

A

Age (class in gpsea.model) age (gpsea.model.Patient property) age_of_death (gpsea.model.VitalStatus attribute) ALIVE (gpsea.model.Status attribute) all_counts (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) all_diseases() (gpsea.model.Cohort method) all_measurements() (gpsea.model.Cohort method) all_patients (gpsea.model.Cohort property) all_phenotypes() (gpsea.model.Cohort method) all_transcript_ids (gpsea.model.Cohort property) all_variant_infos() (gpsea.model.Cohort method) all_variants() (gpsea.model.Cohort method)

allele_count() (in module gpsea.analysis.clf) AlleleCounter (class in gpsea.analysis.clf) allof() (in module gpsea.analysis.predicate) alt (gpsea.model.VariantCoordinates property) AnalysisException AnalysisResult (class in gpsea.analysis) annotate() (gpsea.preprocessing.DefaultImpreciseSvFunctionalAnnotator method) (gpsea.preprocessing.FunctionalAnnotator method) (gpsea.preprocessing.ImpreciseSvFunctionalAnnotator method) (gpsea.preprocessing.ProteinMetadataService method) (gpsea.preprocessing.UniprotProteinMetadataService method) (gpsea.preprocessing.VepFunctionalAnnotator method) anyof() (in module gpsea.analysis.predicate) apply_classifiers_on_individuals() (in module gpsea.analysis.pcats)

B

BaseViewer (class in gpsea.view)

biallelic_classifier() (in module gpsea.analysis.clf) birth() (gpsea.model.Age static method)

C

CACHE_ENV (in module gpsea.config) cat_id (gpsea.analysis.clf.PatientCategory property) Categorization (class in gpsea.analysis.clf) category (gpsea.analysis.clf.Categorization property) cds_end (gpsea.model.TranscriptCoordinates property) cds_start (gpsea.model.TranscriptCoordinates property) change_length (gpsea.model.VariantCoordinates property) change_length() (in module gpsea.analysis.predicate) chrom (gpsea.model.VariantCoordinates property) class_labels (gpsea.analysis.clf.Classifier property) Classifier (class in gpsea.analysis.clf) 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) CohortViewer (class in gpsea.view) COILED_COIL (gpsea.model.FeatureType attribute) compare_genotype_vs_phenotype_score() (gpsea.analysis.pscore.PhenotypeScoreAnalysis method) compare_genotype_vs_phenotypes() (gpsea.analysis.pcats.MultiPhenotypeAnalysis method) compare_genotype_vs_survival() (gpsea.analysis.temporal.SurvivalAnalysis method) complete_records() (gpsea.analysis.MonoPhenotypeAnalysisResult method) COMPOSITIONAL_BIAS (gpsea.model.FeatureType attribute) 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) (gpsea.analysis.temporal.stats.LogRankTest method) (gpsea.analysis.temporal.stats.SurvivalStatistic method) compute_survival() (gpsea.analysis.temporal.Endpoint method) configure_caching_cohort_creator() (in module gpsea.preprocessing) configure_cohort_creator() (in module gpsea.preprocessing)

configure_default_functional_annotator() (in module gpsea.preprocessing) configure_default_protein_metadata_service() (in module gpsea.preprocessing) configure_default_tx_coordinate_service() (in module gpsea.preprocessing) configure_hpo_term_analysis() (in module gpsea.analysis.pcats) 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) ContinuousPartitioning (class in gpsea.analysis) corrected_pvals (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) count() (gpsea.analysis.clf.AlleleCounter method) count_alive() (gpsea.model.Cohort method) count_deceased() (gpsea.model.Cohort method) count_distinct_diseases() (gpsea.model.Cohort method) count_distinct_hpo_terms() (gpsea.model.Cohort method) count_distinct_measurements() (gpsea.model.Cohort method) count_females() (gpsea.model.Cohort method) count_males() (gpsea.model.Cohort method) count_unique_diseases() (gpsea.model.Patient method) count_unique_measurements() (gpsea.model.Patient method) count_unique_phenotypes() (gpsea.model.Patient method) count_unknown_sex() (gpsea.model.Cohort method) count_unknown_vital_status() (gpsea.model.Cohort method) count_with_age_of_last_encounter() (gpsea.model.Cohort method) count_with_disease_onset() (gpsea.model.Cohort 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

data (gpsea.analysis.AnalysisException property) (gpsea.analysis.MonoPhenotypeAnalysisResult property) DATA_COLUMNS (gpsea.analysis.MonoPhenotypeAnalysisResult attribute) days (gpsea.model.Age property) DAYS_IN_MONTH (gpsea.model.Age attribute) DAYS_IN_WEEK (gpsea.model.Age attribute) DAYS_IN_YEAR (gpsea.model.Age attribute) death() (in module gpsea.analysis.temporal.endpoint) DECEASED (gpsea.model.Status attribute) default() (gpsea.io.GpseaJSONEncoder method) DEFAULT_CACHE_PATH (in module gpsea.config) default_filter() (gpsea.analysis.mtc_filter.HpoMtcFilter static method) default_parser() (gpsea.preprocessing.PhenopacketOntologyTermOnsetParser static method) DefaultImpreciseSvFunctionalAnnotator (class in gpsea.preprocessing) DEL (gpsea.model.VariantClass attribute) deprecation_warning() (gpsea.model.FeatureType static method) description (gpsea.analysis.clf.DiseasePresenceClassifier property) (gpsea.analysis.clf.HpoClassifier property) (gpsea.analysis.clf.PatientCategory property) (gpsea.analysis.Partitioning property) (gpsea.analysis.pscore.CountingPhenotypeScorer property) (gpsea.analysis.pscore.DeVriesPhenotypeScorer property) (gpsea.analysis.pscore.MeasurementPhenotypeScorer property)

DeVriesPhenotypeScorer (class in gpsea.analysis.pscore) diagnosis_classifier() (in module gpsea.analysis.clf) Disease (class in gpsea.model) disease_by_id() (gpsea.model.Patient method) disease_onset() (in module gpsea.analysis.temporal.endpoint) DiseaseAnalysis (class in gpsea.analysis.pcats) DiseasePresenceClassifier (class in gpsea.analysis.clf) diseases (gpsea.model.Patient property) DiseaseViewer (class in gpsea.view) distance_to() (gpsea.model.genome.GenomicRegion method) (gpsea.model.genome.Region method) DNA_BINDING (gpsea.model.FeatureType attribute) 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)

Endpoint (class in gpsea.analysis.temporal) endpoint (gpsea.analysis.temporal.SurvivalAnalysisResult property) excluded_diseases() (gpsea.model.Patient method) excluded_phenotypes() (gpsea.model.Patient method) exon() (in module gpsea.analysis.predicate) 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.Formatter method) (gpsea.view.VariantFormatter method) format_coordinates_for_vep_query() (gpsea.preprocessing.VepFunctionalAnnotator static method) Formatter (class in gpsea.view) FRAMESHIFT_VARIANT (gpsea.model.VariantEffect attribute) from_feature_frame() (gpsea.model.ProteinMetadata static method) from_iso8601_period() (gpsea.model.Age static method) from_mapping() (gpsea.model.Genotypes static method) from_measurement_id() (gpsea.analysis.pscore.MeasurementPhenotypeScorer static method) from_patients() (gpsea.model.Cohort static method) from_query_curies() (gpsea.analysis.pscore.CountingPhenotypeScorer static method) from_raw_parts() (gpsea.analysis.clf.Categorization static method) (gpsea.model.Disease static method) (gpsea.model.Patient static method) (gpsea.model.Phenotype static method) from_string() (gpsea.model.FeatureType static method) from_term() (gpsea.model.Phenotype static method) from_uniprot_json() (gpsea.model.ProteinMetadata static method) from_vcf_literal() (gpsea.model.VariantCoordinates static method) from_vcf_symbolic() (gpsea.model.VariantCoordinates static method) FunctionalAnnotationAware (class in gpsea.model) FunctionalAnnotator (class in gpsea.preprocessing)

G

genbank_acc (gpsea.model.genome.Contig property) gene() (in module gpsea.analysis.predicate) 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) GenotypeClassifier (class in gpsea.analysis.clf) Genotyped (class in gpsea.model) Genotypes (class in gpsea.model) genotypes (gpsea.model.Genotyped property) (gpsea.model.Variant property) GESTATIONAL (gpsea.model.Timeline attribute) gestational() (gpsea.model.Age static method) gestational_days() (gpsea.model.Age static method) get_cache_dir_path() (in module gpsea.config) get_categories() (gpsea.analysis.clf.Classifier method) get_categorizations() (gpsea.analysis.clf.Classifier method) (gpsea.analysis.clf.DiseasePresenceClassifier method) (gpsea.analysis.clf.HpoClassifier method) get_category() (gpsea.analysis.clf.Classifier method) get_category_name() (gpsea.analysis.clf.Classifier 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_hgvs_cdna_by_tx_id() (gpsea.model.FunctionalAnnotationAware 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_preferred_tx_annotation() (gpsea.model.FunctionalAnnotationAware method) get_question() (gpsea.analysis.clf.AlleleCounter method) (gpsea.analysis.predicate.VariantPredicate method) get_response() (gpsea.preprocessing.VVMultiCoordinateService method) get_three_prime_utrs() (gpsea.model.TranscriptCoordinates method) get_tx_anno_by_tx_id() (gpsea.model.FunctionalAnnotationAware method)

get_variant_by_key() (gpsea.model.Cohort method) gpsea module gpsea.analysis module gpsea.analysis.clf module gpsea.analysis.mtc_filter module gpsea.analysis.pcats module gpsea.analysis.pcats.stats module gpsea.analysis.predicate module gpsea.analysis.pscore module gpsea.analysis.pscore.stats module gpsea.analysis.temporal module gpsea.analysis.temporal.endpoint module gpsea.analysis.temporal.stats module gpsea.config module gpsea.io module gpsea.model module gpsea.model.genome module gpsea.preprocessing module gpsea.util module gpsea.view module GpseaJSONDecoder (class in gpsea.io) GpseaJSONEncoder (class in gpsea.io) GpseaReport (class in gpsea.view) gt_clf (gpsea.analysis.AnalysisResult property) GT_COL (gpsea.analysis.MonoPhenotypeAnalysisResult attribute)

H

has_sv_info() (gpsea.model.VariantInfo method) has_variant_coordinates() (gpsea.model.VariantInfo 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) hpo_onset() (in module gpsea.analysis.temporal.endpoint) HpoClassifier (class in gpsea.analysis.clf) HpoMtcFilter (class in gpsea.analysis.mtc_filter) 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.Measurement 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_alive (gpsea.model.VitalStatus property) is_censored (gpsea.analysis.temporal.Survival attribute) is_coding() (gpsea.model.TranscriptCoordinates method) is_deceased (gpsea.model.VitalStatus property) is_empty() (gpsea.model.genome.Region method) is_female() (gpsea.model.Sex method)

is_filtered_out() (gpsea.analysis.mtc_filter.PhenotypeMtcResult method) is_gestational (gpsea.model.Age property) is_large_imprecise_sv() (in module gpsea.analysis.predicate) is_male() (gpsea.model.Sex method) is_negative() (gpsea.model.genome.Strand method) is_observed (gpsea.model.Phenotype property) is_ok() (gpsea.preprocessing.PreprocessingValidationResult method) is_passed() (gpsea.analysis.mtc_filter.PhenotypeMtcResult method) is_positive() (gpsea.model.genome.Strand method) is_postnatal (gpsea.model.Age property) 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() (in module gpsea.analysis.predicate) is_structural_variant() (in module gpsea.analysis.predicate) is_unknown (gpsea.model.VitalStatus property) is_unknown() (gpsea.model.Sex method) ISO8601PT (gpsea.model.Age attribute)

L

label (gpsea.analysis.pscore.MeasurementPhenotypeScorer property) (gpsea.model.ProteinMetadata property) (gpsea.model.SampleLabels property) label_summary() (gpsea.model.SampleLabels method) labels (gpsea.model.Patient property) last_menstrual_period() (gpsea.model.Age static method) list_all_diseases() (gpsea.model.Cohort method)

list_all_proteins() (gpsea.model.Cohort method) list_all_variants() (gpsea.model.Cohort method) list_measurements() (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) LogRankTest (class in gpsea.analysis.temporal.stats)

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) Measurement (class in gpsea.model) measurement_by_id() (gpsea.model.Patient method) MeasurementPhenotypeScorer (class in gpsea.analysis.pscore) measurements (gpsea.model.Patient property) meta_label (gpsea.model.SampleLabels property) MISSENSE_VARIANT (gpsea.model.VariantEffect attribute) MNV (gpsea.model.VariantClass attribute) module gpsea gpsea.analysis gpsea.analysis.clf gpsea.analysis.mtc_filter gpsea.analysis.pcats gpsea.analysis.pcats.stats gpsea.analysis.predicate gpsea.analysis.pscore gpsea.analysis.pscore.stats gpsea.analysis.temporal gpsea.analysis.temporal.endpoint gpsea.analysis.temporal.stats gpsea.config gpsea.io gpsea.model gpsea.model.genome gpsea.preprocessing gpsea.util gpsea.view

monoallelic_classifier() (in module gpsea.analysis.clf) MonoPhenotypeAnalysisResult (class in gpsea.analysis) MOTIF (gpsea.model.FeatureType attribute) motifs() (gpsea.model.ProteinMetadata method) mtc_correction (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) mtc_filter_name (gpsea.analysis.pcats.HpoTermAnalysisResult property) mtc_filter_results (gpsea.analysis.pcats.HpoTermAnalysisResult property) mtc_issue (gpsea.analysis.mtc_filter.PhenotypeMtcResult property) MtcStatsViewer (class in gpsea.view) MultiPhenotypeAnalysis (class in gpsea.analysis.pcats) MultiPhenotypeAnalysisResult (class in gpsea.analysis) (class in gpsea.analysis.pcats)

N

n_categorizations() (gpsea.analysis.clf.Classifier method) n_filtered_out() (gpsea.analysis.pcats.HpoTermAnalysisResult method) n_significant_for_alpha() (gpsea.analysis.MultiPhenotypeAnalysisResult method) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult method) n_usable (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) name (gpsea.analysis.clf.DiseasePresenceClassifier property) (gpsea.analysis.clf.HpoClassifier property) (gpsea.analysis.clf.PatientCategory property) (gpsea.analysis.Partitioning property) (gpsea.analysis.pscore.CountingPhenotypeScorer property) (gpsea.analysis.pscore.DeVriesPhenotypeScorer property) (gpsea.analysis.pscore.MeasurementPhenotypeScorer property) (gpsea.analysis.Statistic property) (gpsea.model.Disease property) (gpsea.model.FeatureInfo property) (gpsea.model.genome.Contig property) (gpsea.model.Measurement property)

NEGATIVE (gpsea.model.genome.Strand attribute) NMD_TRANSCRIPT_VARIANT (gpsea.model.VariantEffect 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)

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) onset (gpsea.model.Disease property) (gpsea.model.OnsetAware property) (gpsea.model.Phenotype property)

OnsetAware (class in gpsea.model) open_resource() (in module gpsea.util) open_text_io_handle_for_reading() (in module gpsea.util) open_text_io_handle_for_writing() (in module gpsea.util) opposite() (gpsea.model.genome.Strand method) overlapping_exons (gpsea.model.TranscriptAnnotation property) overlaps_with() (gpsea.model.FeatureInfo method) (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) Partitioning (class in gpsea.analysis) patch (gpsea.model.genome.GenomeBuildIdentifier property) Patient (class in gpsea.model) patient_id (gpsea.model.Patient property) PatientCategory (class in gpsea.analysis.clf) PatientCreator (class in gpsea.preprocessing) PH_COL (gpsea.analysis.MonoPhenotypeAnalysisResult attribute) pheno_clfs (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) PhenopacketOntologyTermOnsetParser (class in gpsea.preprocessing) PhenopacketPatientCreator (class in gpsea.preprocessing) PhenopacketVariantCoordinateFinder (class in gpsea.preprocessing) Phenotype (class in gpsea.model) phenotype (gpsea.analysis.clf.DiseasePresenceClassifier property) (gpsea.analysis.clf.HpoClassifier property) (gpsea.analysis.clf.PhenotypeCategorization property) (gpsea.analysis.clf.PhenotypeClassifier property) (gpsea.analysis.MonoPhenotypeAnalysisResult property) phenotype_by_id() (gpsea.model.Patient method) phenotype_scorer() (gpsea.analysis.pscore.PhenotypeScoreAnalysisResult method) PhenotypeCategorization (class in gpsea.analysis.clf) PhenotypeClassifier (class in gpsea.analysis.clf) PhenotypeMtcFilter (class in gpsea.analysis.mtc_filter) PhenotypeMtcIssue (class in gpsea.analysis.mtc_filter) PhenotypeMtcResult (class in gpsea.analysis.mtc_filter) phenotypes (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) (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) plot_kaplan_meier_curves() (gpsea.analysis.temporal.SurvivalAnalysisResult method) policy (gpsea.preprocessing.PreprocessingValidationResult property) 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) POSTNATAL (gpsea.model.Timeline attribute) postnatal() (gpsea.model.Age static method) postnatal_days() (gpsea.model.Age static method)

postnatal_years() (gpsea.model.Age static method) prepare_classifiers_for_terms_of_interest() (in module gpsea.analysis.clf) prepare_hpo_terms_of_interest() (in module gpsea.analysis.clf) PreprocessingValidationResult (class in gpsea.preprocessing) present_diseases() (gpsea.model.Patient method) present_phenotype_categorization (gpsea.analysis.clf.DiseasePresenceClassifier property) (gpsea.analysis.clf.HpoClassifier property) (gpsea.analysis.clf.PhenotypeClassifier property) present_phenotype_category (gpsea.analysis.clf.PhenotypeClassifier property) present_phenotypes() (gpsea.model.Patient method) process() (gpsea.preprocessing.CohortCreator method) (gpsea.preprocessing.PatientCreator method) (gpsea.preprocessing.PhenopacketOntologyTermOnsetParser method) (gpsea.preprocessing.PhenopacketPatientCreator method) (gpsea.view.CohortVariantViewer method) (gpsea.view.CohortViewer method) (gpsea.view.DiseaseViewer method) (gpsea.view.MtcStatsViewer method) (gpsea.view.ProteinVariantViewer method) process_response() (gpsea.preprocessing.VepFunctionalAnnotator method) PROTEIN_ALTERING_VARIANT (gpsea.model.VariantEffect attribute) protein_effect_location (gpsea.model.TranscriptAnnotation property) protein_feature() (in module gpsea.analysis.predicate) protein_feature_ends (gpsea.view.ProteinVisualizable property) protein_feature_names (gpsea.view.ProteinVisualizable property) protein_feature_starts (gpsea.view.ProteinVisualizable property) protein_feature_type() (in module gpsea.analysis.predicate) 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) protein_region() (in module gpsea.analysis.predicate) ProteinFeature (class in gpsea.model) ProteinMetadata (class in gpsea.model) ProteinMetadataService (class in gpsea.preprocessing) ProteinVariantViewer (class in gpsea.view) ProteinVisualizable (class in gpsea.view) ProteinVisualizer (class in gpsea.view) pval (gpsea.analysis.MonoPhenotypeAnalysisResult property) (gpsea.analysis.StatisticResult property) pvals (gpsea.analysis.MultiPhenotypeAnalysisResult property) (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() (in module gpsea.analysis.predicate) 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) 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.MeasurementPhenotypeScorer method) (gpsea.analysis.pscore.PhenotypeScorer method) SEQUENCE_VARIANT (gpsea.model.VariantEffect attribute) Sex (class in gpsea.model) sex (gpsea.model.Patient property) sex_classifier() (in module gpsea.analysis.clf) significant_phenotype_indices() (gpsea.analysis.MultiPhenotypeAnalysisResult method) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult method) 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_SINCE_ONE_GENOTYPE_HAD_ZERO_OBSERVATIONS (gpsea.analysis.mtc_filter.HpoMtcFilter attribute) SNV (gpsea.model.VariantClass attribute) 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) Statistic (class in gpsea.analysis) statistic (gpsea.analysis.AnalysisResult property) (gpsea.analysis.StatisticResult property)

statistic_result() (gpsea.analysis.MonoPhenotypeAnalysisResult method) statistic_results (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) StatisticResult (class in gpsea.analysis) Status (class in gpsea.model) status (gpsea.model.VitalStatus attribute) STOP_GAINED (gpsea.model.VariantEffect attribute) STOP_LOST (gpsea.model.VariantEffect attribute) STOP_RETAINED_VARIANT (gpsea.model.VariantEffect attribute) 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() (in module gpsea.analysis.predicate) Summarizable (class in gpsea.analysis) summarize() (gpsea.analysis.clf.Classifier method) (gpsea.analysis.Partitioning method) (gpsea.analysis.Summarizable method) (gpsea.preprocessing.PreprocessingValidationResult method) summarize_classes() (gpsea.analysis.clf.Classifier method) summarize_hpo_analysis() (in module gpsea.view) summary() (gpsea.analysis.Summarizable method) supports_shape (gpsea.analysis.pcats.stats.CountStatistic property) (gpsea.analysis.pcats.stats.FisherExactTest property) Survival (class in gpsea.analysis.temporal) SurvivalAnalysis (class in gpsea.analysis.temporal) SurvivalAnalysisResult (class in gpsea.analysis.temporal) SurvivalStatistic (class in gpsea.analysis.temporal.stats) sv_info (gpsea.model.VariantInfo property) symbol (gpsea.model.genome.Strand property) SYNONYMOUS_VARIANT (gpsea.model.VariantEffect attribute)

T

term_id (gpsea.analysis.pscore.MeasurementPhenotypeScorer property) terms_to_test (gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter property) test() (gpsea.analysis.clf.Classifier method) (gpsea.analysis.clf.DiseasePresenceClassifier method) (gpsea.analysis.clf.HpoClassifier method) (gpsea.analysis.predicate.VariantPredicate method) test_result (gpsea.model.Measurement property) 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) Timeline (class in gpsea.model) timeline (gpsea.model.Age property) 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) TOPOLOGICAL_DOMAIN (gpsea.model.FeatureType attribute) total_patient_count (gpsea.model.Cohort property)

total_tests (gpsea.analysis.MultiPhenotypeAnalysisResult property) (gpsea.analysis.pcats.MultiPhenotypeAnalysisResult property) transcript() (in module gpsea.analysis.predicate) 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) TRANSLOCATION (gpsea.model.VariantClass attribute) TRANSMEMBRANE (gpsea.model.FeatureType attribute) Transposable (class in gpsea.model.genome) transpose_coordinate() (in module gpsea.model.genome) true() (in module gpsea.analysis.predicate) TTestStatistic (class in gpsea.analysis.pscore.stats) tx_annotations (gpsea.model.FunctionalAnnotationAware property) (gpsea.model.Variant property)

U

ucsc_name (gpsea.model.genome.Contig property) UniprotProteinMetadataService (class in gpsea.preprocessing) unit (gpsea.model.Measurement property)

UNKNOWN (gpsea.model.Status attribute) UNKNOWN_SEX (gpsea.model.Sex attribute) UPSTREAM_GENE_VARIANT (gpsea.model.VariantEffect attribute) UseAllTermsMtcFilter (class in gpsea.analysis.mtc_filter)

V

value (gpsea.analysis.temporal.Survival attribute) variable_name (gpsea.analysis.clf.DiseasePresenceClassifier property) (gpsea.analysis.clf.HpoClassifier property) (gpsea.analysis.Partitioning property) (gpsea.analysis.pscore.CountingPhenotypeScorer property) (gpsea.analysis.pscore.DeVriesPhenotypeScorer property) (gpsea.analysis.pscore.MeasurementPhenotypeScorer property) Variant (class in gpsea.model) variant_class (gpsea.model.ImpreciseSvInfo property) (gpsea.model.VariantCoordinates property) (gpsea.model.VariantInfo property) variant_class() (in module gpsea.analysis.predicate) variant_coordinates (gpsea.model.VariantInfo property) variant_effect() (in module gpsea.analysis.predicate) 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() (in module gpsea.analysis.predicate) variant_locations (gpsea.view.ProteinVisualizable property) variant_locations_counted_absolute (gpsea.view.ProteinVisualizable property) 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) variants (gpsea.model.Patient property) VariantTranscriptVisualizer (class in gpsea.view) VariantValidatorDecodeException VepFunctionalAnnotator (class in gpsea.preprocessing) verify_term_id() (gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter static method) vital_status (gpsea.model.Patient property) VitalStatus (class in gpsea.model) VVHgvsVariantCoordinateFinder (class in gpsea.preprocessing) VVMultiCoordinateService (class in gpsea.preprocessing)

W

with_strand() (gpsea.model.genome.GenomicRegion method) (gpsea.model.genome.Transposable method)

wrap_scoring_function() (gpsea.analysis.pscore.PhenotypeScorer static method) write() (gpsea.view.GpseaReport method)

Z

ZINC_FINGER (gpsea.model.FeatureType attribute)