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Functions1,294 in github.com/broadinstitute/gnomad-browser

⨍ Functions 1,294◇ Types & classes 131
↓ 1 callersFunctionget_exons
Filter GENCODE table to exons and format fields.
data-pipeline/src/data_pipeline/data_types/gene.py:33
↓ 1 callersFunctionget_genes
Filter GENCODE table to genes and format fields.
data-pipeline/src/data_pipeline/data_types/gene.py:60
↓ 1 callersFunctionget_gnomad_v2_variants
Get locus/alleles for all gnomAD v2 variants.
data-pipeline/caids/export_vcfs.py:26
↓ 1 callersFunctionget_gnomad_v3_variants
Get locus/alleles for all gnomAD v3 variants.
data-pipeline/caids/export_vcfs.py:17
↓ 1 callersFunctionget_gnomad_v4_variants
Get locus/alleles for all gnomAD v4 variants.
data-pipeline/caids/export_vcfs.py:8
↓ 1 callersFunctionget_index_fields
(table, index_fields)
data-pipeline/src/data_pipeline/helpers/elasticsearch_export.py:85
↓ 1 callersFunctionget_tag_from_git_revision
()
deploy/deployctl/tag.py:5
↓ 1 callersFunctionget_transcripts
Filter GENCODE table to transcripts and format fields.
data-pipeline/src/data_pipeline/data_types/gene.py:187
↓ 1 callersFunctionget_variants
Get locus/alleles for all variants in the given dataset.
data-pipeline/caids/export_vcfs.py:55
↓ 1 callersFunctiongraphQLApi
({ context }: any)
graphql-api/src/graphql/graphql-api.ts:120
↓ 1 callersFunctiongroupPopulations
(populations: any, datasetId: DatasetId)
browser/src/VariantPage/HGDPPopulationsTable.tsx:219
↓ 1 callersFunctiongroupPopulations
(populations: any)
browser/src/VariantPage/TGPPopulationsTable.tsx:57
↓ 1 callersFunctiongroupPopulations
( populations: LocalAncestryPopulation[] )
browser/src/VariantPage/LocalAncestryPopulationsTable.tsx:34
↓ 1 callersFunctiongtf2bed
(gtf: hl.Table)
reads/reference-data/gtf2bed.py:7
↓ 1 callersFunctionhaplotypeFreqEM
(genotypeCounts: any)
graphql-api/src/queries/variant-cooccurrence-queries.ts:152
↓ 1 callersFunctionhas1000GenomesPopulationFrequencies
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1106
↓ 1 callersFunctionhasAlleleBalance
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1109
↓ 1 callersFunctionhasConstraints
(datsetId: DatasetId)
dataset-metadata/metadata.ts:1043
↓ 1 callersFunctionhasExome
(datsetId: DatasetId)
dataset-metadata/metadata.ts:1051
↓ 1 callersFunctionhasJointFrequencyData
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1160
↓ 1 callersFunctionhasLocalAncestryPopulations
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1076
↓ 1 callersFunctionhasNonCodingReadData
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1128
↓ 1 callersFunctionhasNonzeroTotalMetrics
(indexData: any)
graphql-api/src/esPoll.ts:14
↓ 1 callersFunctionhasRelatedVariants
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1111
↓ 1 callersFunctionhasVRSData
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1182
↓ 1 callersFunctionhgvsp_from_consequence_amino_acids
(csq)
data-pipeline/src/data_pipeline/data_types/variant/transcript_consequence/hgvs.py:33
↓ 1 callersFunctionimportAllHeadshots
(webpackContext)
browser/src/TeamPage/headshotLoader.js:2
↓ 1 callersFunctionimport_caids
Import CAIDs created by `get_caids.py` into a Hail Table. :param caids_url: URL of directory/prefix where CAID files are located. :param
data-pipeline/caids/import_caids.py:8
↓ 1 callersFunctionimport_gencode
(path, reference_genome)
data-pipeline/src/data_pipeline/data_types/gene.py:252
↓ 1 callersFunctionimport_hgnc
(path)
data-pipeline/src/data_pipeline/data_types/gene.py:287
↓ 1 callersFunctionimport_mnv_file
(path, **kwargs)
data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_mnvs.py:30
↓ 1 callersFunctionimport_three_bp_mnv_file
(path, **kwargs)
data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_mnvs.py:200
↓ 1 callersFunctionisFulfilled
(promise: PromiseSettledResult<T>)
graphql-api/src/esPoll.ts:8
↓ 1 callersFunctionisProteinMitochondrialGeneConstraint
( constraint: MitochondrialGeneConstraint )
browser/src/ConstraintTable/MitochondrialConstraintTable.tsx:12
↓ 1 callersFunctionisSVs
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1099
↓ 1 callersFunctionisV4CNVs
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1149
↓ 1 callersFunctionisVariantEligibleForCooccurrence
(variant: any, datasetId: any)
browser/src/VariantPage/VariantRelatedVariants.tsx:35
↓ 1 callersFunctionisVrsId
(id: string)
graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts:59
↓ 1 callersFunctionisWhitelistedIP
(ip: string)
graphql-api/src/whitelist.ts:27
↓ 1 callersFunctionis_transient_error
(e)
data-pipeline/caids/get_caids.py:58
↓ 1 callersFunctionjoint_freq_index_key
(subset=None, pop=None, sex=None, raw=False)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:319
↓ 1 callersFunctionlegendLabels
(colorBy: ColorBy, keys: string[])
browser/src/ShortTandemRepeatPage/ShortTandemRepeatAlleleSizeDistributionPlot.tsx:111
↓ 1 callersMethodloadAllTracks
()
browser/src/ReadData/ReadData.tsx:352
↓ 1 callersMethodloadInitialTracks
()
browser/src/ReadData/ReadData.tsx:342
↓ 1 callersMethodloadPreferences
()
browser/src/userPreferences.ts:4
↓ 1 callersFunctionloadWhitelist
()
graphql-api/src/whitelist.ts:14
↓ 1 callersFunctionlofTooltipContent
(loeuf: number, percentile: number | null)
browser/src/ConstraintTable/GnomadConstraintTable.tsx:82
↓ 1 callersFunctionlofteeAnnotationDescription
(consequence: any)
browser/src/MitochondrialVariantPage/MitochondrialVariantTranscriptConsequence.tsx:76
↓ 1 callersFunctionlofteeAnnotationDescription
(consequence: any)
browser/src/VariantPage/TranscriptConsequence.tsx:76
↓ 1 callersFunctionlofteeAnnotationMarker
(consequence: any)
browser/src/MitochondrialVariantPage/MitochondrialVariantTranscriptConsequence.tsx:64
↓ 1 callersFunctionlofteeAnnotationMarker
(consequence: any)
browser/src/VariantPage/TranscriptConsequence.tsx:64
↓ 1 callersFunctionlogAnalyticsEvent
( eventName: string, eventCategory: string, eventLabel: string )
browser/src/analytics.ts:1
↓ 1 callersFunctionmain
()
deploy/deployctl/__main__.py:16
↓ 1 callersFunctionmain
()
development/scripts/get_object_metadata.py:72
↓ 1 callersFunctionmain
(argv)
data-pipeline/src/data_pipeline/pipelines/check_missingness.py:46
↓ 1 callersFunctionmain
(argv)
data-pipeline/src/data_pipeline/pipelines/export_to_elasticsearch.py:29
↓ 1 callersFunctionmain
()
data-pipeline/caids/import_caids.py:31
↓ 1 callersFunctionmain
()
data-pipeline/caids/export_vcfs.py:88
↓ 1 callersFunctionmain
()
data-pipeline/caids/get_caids.py:229
↓ 1 callersFunctionmain
()
reads/reference-data/gtf2bed.py:78
↓ 1 callersFunctionmakePrediction
({ p_compound_heterozygous, genotype_counts, }: CooccurrenceForPopulation)
browser/src/VariantCooccurrencePage/VariantCooccurrencePage.tsx:114
↓ 1 callersFunctionmake_dir
(path)
data-pipeline/src/data_pipeline/helpers/write_schemas.py:8
↓ 1 callersFunctionmaxAlleleSizeDistributionRepeats
( shortTandemRepeatOrAdjacentRepeat: ShortTandemRepeat | ShortTandemRepeatAdjacentRepeat )
browser/src/ShortTandemRepeatPage/shortTandemRepeatHelpers.ts:163
↓ 1 callersFunctionmaxGenotypeDistributionRepeats
( shortTandemRepeat: ShortTandemRepeat | ShortTandemRepeatAdjacentRepeat )
browser/src/ShortTandemRepeatPage/shortTandemRepeatHelpers.ts:172
↓ 1 callersFunctionmergeOverlappingRegions
(regions: any)
browser/src/GenePage/TranscriptsTissueExpressionPlot.tsx:10
↓ 1 callersFunctionmetricsIncludeLowQualityGenotypes
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1103
↓ 1 callersMethodmodified_time
(self, path)
data-pipeline/src/data_pipeline/pipeline.py:39
↓ 1 callersFunctionnestPopulations
(populations: CopyNumberVariantPopulation[])
browser/src/CopyNumberVariantPage/CopyNumberVariantPopulationsTable.tsx:19
↓ 1 callersFunctionnestPopulations
(populations: any)
browser/src/StructuralVariantPage/StructuralVariantPopulationsTable.tsx:7
↓ 1 callersFunctionnestPopulations
(populations: any)
browser/src/VariantPage/GnomadPopulationsTable.tsx:35
↓ 1 callersFunctionnoExpectedVariants
(gnomadConstraint: GnomadConstraint | null)
browser/src/ConstraintTable/ConstraintTable.tsx:61
↓ 1 callersFunctionnoPredictionPossible
({ genotype_counts, p_compound_heterozygous, }: CooccurrenceForPopulation)
browser/src/VariantCooccurrencePage/VariantCooccurrencePage.tsx:176
↓ 1 callersFunctionnormalizeCooccurrenceData
(cooccurrenceData: any)
browser/src/VariantCooccurrencePage/VariantCooccurrencePage.tsx:445
↓ 1 callersFunctionnormalizedStringify
(input: JSONAble)
graphql-api/src/graphql/resolvers/va.ts:122
↓ 1 callersFunctionparseMitochondrialGeneConstraintTSV
( rawTSV: string )
graphql-api/src/graphql/resolvers/mitochondrial-constraint.ts:106
↓ 1 callersFunctionparseMitochondrialRegionConstraintTSV
( rawTSV: string, geneSymbols: string[] )
graphql-api/src/graphql/resolvers/mitochondrial-constraint.ts:152
↓ 1 callersFunctionparseProxyConfig
(config: any)
graphql-api/src/config.ts:6
↓ 1 callersFunctionparseProxyConfig
(config)
reads/src/server.js:11
↓ 1 callersFunctionparse_clinvar_xml_to_tsv
( input_xml_path, output_tsv_path, parse_variant_function, )
data-pipeline/src/data_pipeline/datasets/clinvar.py:192
↓ 1 callersFunctionpopulation_frequencies_expression
(ds, freq_index_dict, subset)
data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_variants.py:15
↓ 1 callersFunctionprepareData
({ datasetId, metric, variant, }: { datasetId: DatasetId metric: string variant: Variant })
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:432
↓ 1 callersFunctionprepareDataExac
({ metric, variant }: any)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:388
↓ 1 callersFunctionprepareDataGnomadV2
({ metric, variant }: any)
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:248
↓ 1 callersFunctionprepareDataGnomadV3
({ metric, genome }: { metric: string; genome: SequencingType })
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:230
↓ 1 callersFunctionprepareDataGnomadV4
({ metric, variant }: { metric: string; variant: Variant })
browser/src/VariantPage/VariantSiteQualityMetrics.tsx:190
↓ 1 callersFunctionprepareOverallData
({ datasetId, includeExomes, includeGenomes }: any)
browser/src/VariantPage/GnomadAgeDistribution.tsx:85
↓ 1 callersFunctionprepareVariantData
({ includeExomes, includeGenomes, includeHeterozygotes, includeHomozygotes, variant, }: any)
browser/src/VariantPage/GnomadAgeDistribution.tsx:38
↓ 1 callersFunctionprepare_base_level_pext
(base_level_pext_path)
data-pipeline/src/data_pipeline/data_types/pext.py:83
↓ 1 callersFunctionprepare_gnomad_v4_variants_joint_frequency_helper
(variants_joint_frequency_path)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:315
↓ 1 callersFunctionreadJsonFromFile
(path: string, useCompression = false)
graphql-api/src/queries/helpers/json-cache.ts:45
↓ 1 callersFunctionreadJsonFromFileGcs
( path: string, bucket: Bucket, useCompression = false )
graphql-api/src/queries/helpers/json-cache.ts:86
↓ 1 callersFunctionread_bases_tsv
(filename)
data-pipeline/src/data_pipeline/data_types/pext.py:73
↓ 1 callersFunctionreadsIncludeLowQualityGenotypes
(datasetId: DatasetId)
dataset-metadata/metadata.ts:1133
↓ 1 callersFunctionregionColor
(region: any)
browser/src/RegionalConstraintTrack.tsx:40
↓ 1 callersFunctionregionsHaveExomeCoverage
(datsetId: DatasetId)
dataset-metadata/metadata.ts:1062
↓ 1 callersFunctionregionsHaveGenomeCoverage
(datsetId: DatasetId)
dataset-metadata/metadata.ts:1065
↓ 1 callersFunctionregisterConsequences
(consequences: any)
browser/src/vepConsequences.ts:204
↓ 1 callersMethodremoveNotification
(id: any)
browser/src/Notifications.tsx:91
↓ 1 callersMethodrender
()
browser/src/CopyNumberVariantPage/CNVPopulationsTable.tsx:179
↓ 1 callersFunctionrenderAnswer
()
browser/help/faq/mitochondrial-dna/how-many-samples-are-in-each-mtdna-haplogroup-for-each-nuclear-ancestry-population.tsx:136
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