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

⨍ Functions 1,294◇ Types & classes 131
↓ 2 callersFunctionrenderNumber
(number: any)
browser/src/RegionalConstraintTrack.tsx:56
↓ 2 callersFunctionrenderNumber
(number: number | null | undefined)
browser/src/RegionalGenomicConstraintTrack.tsx:114
↓ 2 callersFunctionrenderPopAF
(af: number)
browser/src/VariantPage/PopulationsTable.tsx:71
↓ 2 callersFunctionrenderPopSF
(sf: number | string)
browser/src/CopyNumberVariantPage/CNVPopulationsTable.tsx:58
↓ 2 callersFunctionrenderTrackLeftPanel
(constraintWidth: number)
browser/src/RegionalGenomicConstraintTrack.tsx:137
↓ 2 callersFunctionrenderVariantFlag
(variant: any, exomeOrGenome: any)
browser/src/MNVPage/MNVConstituentSNVFrequencyTable.tsx:30
↓ 2 callersFunctionresolveVAAllele
(obj: any, _args: any, _ctx: any)
graphql-api/src/graphql/resolvers/va.ts:149
↓ 2 callersFunctionresolveVACohortAlleleFrequencies
( obj: any, args: any, ctx: any, frequencyField: 'exome' | 'genome' )
graphql-api/src/graphql/resolvers/va.ts:384
↓ 2 callersFunctionscale
(position: any)
browser/src/GenePage/TranscriptsTissueExpressionPlot.tsx:41
↓ 2 callersFunctionscrollToAnchorOrStartOfPage
(location: any)
browser/src/App.tsx:16
↓ 2 callersMethodsetSortBy
(sortBy: any)
browser/src/MitochondrialVariantPage/MitochondrialVariantHaplogroupFrequenciesTable.tsx:68
↓ 2 callersFunctionshapeMitochondrialVariantSummary
(context: any)
graphql-api/src/queries/mitochondrial-variant-datasets/gnomad-v3-mitochondrial-variant-queries.ts:74
↓ 2 callersFunctionshape_phase_info_data
(phase_info)
data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_variant_cooccurrence.py:26
↓ 2 callersFunctionslugify
(string: any)
browser/src/help/slugify.ts:1
↓ 2 callersFunctionsortedTranscripts
( transcripts: GenericTranscript[], firstTranscriptId: string | undefined )
browser/src/GenePage/sortedTranscripts.ts:13
↓ 2 callersFunctionsplit_position_end
(position)
data-pipeline/src/data_pipeline/datasets/exac/exac_variants.py:262
↓ 2 callersFunctionsplit_position_start
(position)
data-pipeline/src/data_pipeline/datasets/exac/exac_variants.py:255
↓ 2 callersFunctionsubset_filter
(subset)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_variants.py:48
↓ 2 callersFunctiontickFormat
(n: number)
browser/src/ShortTandemRepeatPage/ShortTandemRepeatAlleleSizeDistributionPlot.tsx:116
↓ 2 callersFunctiontruncate_clinvar_variant_ids
(ds)
data-pipeline/src/data_pipeline/helpers/datasets_config.py:44
↓ 2 callersFunctionuseTableSort
( columnSpecifiers: ColumnSpecifier<RowData>[], defaultSortKey: keyof RowData, rowData: RowData[] )
browser/src/useTableSort.tsx:44
↓ 2 callersMethodwrite
(self, path, overwrite)
data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_mnvs.py:17
↓ 2 callersFunctionxPosition
(chrom: any, pos: any)
graphql-api/src/graphql/resolvers/region.ts:12
↓ 2 callersFunctionx_position
(chrom, position)
data-pipeline/src/data_pipeline/datasets/gnomad_v4/gnomad_v4_cnvs.py:6
↓ 1 callersFunctionRow
({ data: { highlightedVariant, isPositionDefined, onHover, scalePosition, trackColor,
browser/src/StructuralVariantList/StructuralVariantTracks.tsx:26
↓ 1 callersFunction_associate_condition_with_medgen_id
(submission_element, trait_mapping_list_element, trait_element)
data-pipeline/src/data_pipeline/datasets/clinvar.py:99
↓ 1 callersFunction_determine_mapping_and_preferred_name_element
(trait_element, submission_element, trait_mapping_list_element)
data-pipeline/src/data_pipeline/datasets/clinvar.py:82
↓ 1 callersFunction_elasticsearch_mapping_for_hail_type
(dtype)
data-pipeline/src/data_pipeline/helpers/elasticsearch_export.py:24
↓ 1 callersFunction_encode_allele
(allele: hl.expr.StringExpression)
data-pipeline/src/data_pipeline/data_types/variant/variant_id.py:49
↓ 1 callersFunction_fetchGeneById
(esClient: any, geneId: any, referenceGenome: any)
graphql-api/src/queries/gene-queries.ts:11
↓ 1 callersFunction_fetchMitochondrialGenomeCoverageForGene
( esClient: any, datasetId: any, gene: any )
graphql-api/src/queries/mitochondrial-coverage-queries.ts:74
↓ 1 callersFunction_fetchMitochondrialVariantsByGene
(esClient: any, datasetId: DatasetId, gene: any)
graphql-api/src/queries/mitochondrial-variant-queries.ts:45
↓ 1 callersFunction_format_read
(read, index, locus)
reads/reads-data/create_short_tandem_repeat_reads_db.py:8
↓ 1 callersFunction_get_gnomad_variants
( gnomad_exome_variants_path=None, gnomad_genome_variants_path=None, gnomad_mitochondrial_variants_path=No
data-pipeline/src/data_pipeline/datasets/clinvar.py:331
↓ 1 callersFunction_get_index_field
(field)
data-pipeline/src/data_pipeline/helpers/elasticsearch_export.py:86
↓ 1 callersFunction_grouped
(arr: hl.expr.ArrayExpression, group_size: hl.expr.Int32Expression)
data-pipeline/src/data_pipeline/data_types/variant/variant_id.py:45
↓ 1 callersFunction_parse_allele_count_histogram_section
(cohort_key, distribution)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:70
↓ 1 callersFunction_parse_allele_scatter_plot_distribution
(distribution)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:96
↓ 1 callersFunction_parse_allele_scatter_plot_histogram_section
(cohort_key, distribution)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:100
↓ 1 callersFunction_parse_reference_regions
(regions)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:119
↓ 1 callersFunction_parse_submission
(submission_element, trait_mapping_list_element)
data-pipeline/src/data_pipeline/datasets/clinvar.py:112
↓ 1 callersFunction_prepare_disease_repeat_size_classifications
(disease)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:47
↓ 1 callersFunction_prepare_histogram
(histogram)
data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_short_tandem_repeats.py:13
↓ 1 callersFunctionaddCohortToAlleleSizeDistribution
( cohort: AlleleSizeDistributionCohort, colorBy: ColorBy | null, distribution: Record<string, AlleleSize
browser/src/ShortTandemRepeatPage/shortTandemRepeatHelpers.ts:25
↓ 1 callersFunctionaddCohortToGenotypeDistribution
( cohort: GenotypeDistributionCohort, distribution: Record<string, GenotypeDistributionItem> )
browser/src/ShortTandemRepeatPage/shortTandemRepeatHelpers.ts:99
↓ 1 callersFunctionaddPopulationNames
(populations: CopyNumberVariantPopulation[])
browser/src/CopyNumberVariantPage/CopyNumberVariantPopulationsTable.tsx:48
↓ 1 callersFunctionaddPopulationNames
(populations: any)
browser/src/StructuralVariantPage/StructuralVariantPopulationsTable.tsx:45
↓ 1 callersFunctionaddPopulationNames
(populations: any)
browser/src/VariantPage/GnomadPopulationsTable.tsx:20
↓ 1 callersFunctionaddPopulationNames
(populations: any, datasetId: DatasetId)
browser/src/VariantPage/HGDPPopulationsTable.tsx:200
↓ 1 callersFunctionaddPopulationNames
(populations: any)
browser/src/VariantPage/TGPPopulationsTable.tsx:42
↓ 1 callersFunctionaddPopulationNames
(populations: PopulationWithLocalAncestryPopulations[])
browser/src/VariantPage/LocalAncestryPopulationsTable.tsx:22
↓ 1 callersFunctionaddSubcohorts
( cohortsWithoutSubcohorts: CohortAlleleFrequencyWithoutSubcohorts[] )
graphql-api/src/graphql/resolvers/va.ts:361
↓ 1 callersFunctionadd_liftover_document_id
(ds)
data-pipeline/src/data_pipeline/helpers/datasets_config.py:50
↓ 1 callersFunctionalgorithmLabel
(algorithm: string)
browser/src/StructuralVariantPage/StructuralVariantAttributeList.tsx:79
↓ 1 callersFunctionannotateVariantsWithPext
(variants: any, pext: any)
browser/src/GenePage/VariantsInGene.tsx:308
↓ 1 callersFunctionannotate_with_histograms
(ds, histograms)
data-pipeline/src/data_pipeline/datasets/gnomad_sv_v2.py:241
↓ 1 callersFunctionapiCallsMatching
( mockFetch: Mock<any>, callIdentifier: string )
tests/__helpers__/apiCall.tsx:5
↓ 1 callersFunctionapplyRateLimits
(request: any)
graphql-api/src/graphql/rate-limiting.ts:46
↓ 1 callersFunctionapply_services
(name: str, browser_deployment: str = None)
deploy/deployctl/subcommands/ingress_demo.py:88
↓ 1 callersFunctionapply_services
(browser_deployment: str = None)
deploy/deployctl/subcommands/ingress_production.py:45
↓ 1 callersFunctionareVariablesEqual
(variables: any, otherVariables: any)
browser/src/Query.tsx:6
↓ 1 callersFunctionassertCooccurrenceShouldBeAvailable
(variants: any)
graphql-api/src/queries/variant-cooccurrence-queries.ts:39
↓ 1 callersFunctionbuildPriorityMapping
()
browser/src/ClinvarVariantsTrack/clinvarVariantCategories.ts:32
↓ 1 callersFunctioncalculateACHet
(haplogroups: Haplogroup[])
browser/src/MitochondrialVariantPage/MitochondrialVariantHaplogroupFrequenciesTable.tsx:53
↓ 1 callersFunctioncalculateACHom
(haplogroups: Haplogroup[])
browser/src/MitochondrialVariantPage/MitochondrialVariantHaplogroupFrequenciesTable.tsx:50
↓ 1 callersFunctioncalculateAN
(haplogroups: Haplogroup[])
browser/src/MitochondrialVariantPage/MitochondrialVariantHaplogroupFrequenciesTable.tsx:47
↓ 1 callersFunctioncancelable
(promise: any)
browser/src/useRequest.ts:3
↓ 1 callersFunctioncancelable
(promise: any)
browser/src/Query.tsx:15
↓ 1 callersFunctioncheckGeneLink
(transcript_consequences: TranscriptConsequence[] | null)
browser/src/VariantPage/VariantPage.tsx:787
↓ 1 callersFunctioncheckIndent
(idString: string)
browser/src/DataPage/TableOfContents.tsx:32
↓ 1 callersFunctionchooseIdField
(variantId: string)
graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts:61
↓ 1 callersFunctionclean_deployment
(name: str)
deploy/deployctl/subcommands/browser_deployments.py:268
↓ 1 callersFunctionclinvarVariantConsequenceCategory
(variant: any)
browser/src/ClinvarVariantsTrack/clinvarVariantCategories.ts:98
↓ 1 callersFunctioncohortForSubset
(subset: Subset, frequencyField: 'exome' | 'genome')
graphql-api/src/graphql/resolvers/va.ts:238
↓ 1 callersFunctioncollect_gene_exons
(gene_exons)
data-pipeline/src/data_pipeline/data_types/gene.py:84
↓ 1 callersFunctioncollect_transcript_exons
(transcript_exons)
data-pipeline/src/data_pipeline/data_types/gene.py:210
↓ 1 callersFunctioncolorForValue
(colorBy: ColorBy | null, value: string)
browser/src/ShortTandemRepeatPage/ShortTandemRepeatAlleleSizeDistributionPlot.tsx:114
↓ 1 callersFunctioncomplexTypeLabel
(complexType: string)
browser/src/StructuralVariantPage/StructuralVariantAttributeList.tsx:82
↓ 1 callersFunctioncontig_number
(contig: hl.expr.StringExpression)
data-pipeline/src/data_pipeline/data_types/locus.py:8
↓ 1 callersFunctioncountClinvarVariantsInRegion
( esClient: any, referenceGenome: any, region: any )
graphql-api/src/queries/clinvar-variant-queries.ts:45
↓ 1 callersFunctioncountVariantsInRegion
(esClient: any, datasetId: DatasetId, region: any)
graphql-api/src/queries/variant-queries.ts:111
↓ 1 callersFunctioncreateDirectoryIfNotExists
(path: string)
graphql-api/src/queries/helpers/json-cache.ts:13
↓ 1 callersFunctioncreateExpectedPopulationColumns
(populations: PopulationId[])
browser/src/VariantList/ExportVariantsButton.spec.tsx:41
↓ 1 callersFunctioncreate_deployment
(name: str, browser_tag: str = None, api_tag: str = None, demo: bool = False)
deploy/deployctl/subcommands/browser_deployments.py:176
↓ 1 callersFunctioncreate_logger
()
data-pipeline/src/data_pipeline/helpers/logging.py:8
↓ 1 callersFunctioncreate_short_tandem_repeat_reads_db
(input_path, output_path)
reads/reads-data/create_short_tandem_repeat_reads_db.py:49
↓ 1 callersFunctioncreate_task
(part_url)
data-pipeline/caids/get_caids.py:176
↓ 1 callersFunctiondecompose_table
(table)
data-pipeline/src/data_pipeline/pipelines/check_missingness.py:14
↓ 1 callersFunctiondetermine_deployment_pool
(path: str)
deploy/deployctl/subcommands/browser_deployments.py:142
↓ 1 callersFunctiondownloadElementAsPNG
(elementID: string)
browser/src/StatsPage/DownloadFigure.tsx:7
↓ 1 callersFunctiondraggable
(C: any)
browser/src/RegionViewer/ZoomRegionOverview.tsx:13
↓ 1 callersFunctionemptyAncestries
(ancestry: PopulationId)
browser/src/VariantList/mergeExomeAndGenomeData.ts:9
↓ 1 callersMethodexportPlot
()
browser/src/CoverageTrack.tsx:137
↓ 1 callersFunctionexportVariantsToCsv
(variants: any, baseFileName: any)
browser/src/StructuralVariantList/ExportStructuralVariantsButton.tsx:74
↓ 1 callersFunctionexportVariantsToCsv
( variants: VariantTableVariant[], datasetId: DatasetId, baseFileName: string )
browser/src/VariantList/ExportVariantsButton.tsx:232
↓ 1 callersFunctionexportVariantsToCsv
(variants: CopyNumberVariant[], baseFileName: any)
browser/src/CopyNumberVariantList/ExportCopyNumberVariantsButton.tsx:45
↓ 1 callersFunctionexportVariantsToCsv
(variants: any, baseFileName: any, includeGene: any)
browser/src/MitochondrialVariantList/ExportMitochondrialVariantsButton.tsx:67
↓ 1 callersFunctionexport_datasets
(elasticsearch_host, elasticsearch_auth, datasets)
data-pipeline/src/data_pipeline/pipelines/export_to_elasticsearch.py:16
↓ 1 callersFunctionexport_table_to_elasticsearch
( table, host, index, *, auth=None, block_size=5000, id_field=None, index_fiel
data-pipeline/src/data_pipeline/helpers/elasticsearch_export.py:96
↓ 1 callersFunctionexport_vcfs
Export locus and alleles fields from a Hail Table to a sharded VCF. :param ds: Hail Table. :param output_url: URL to directory/prefix wh
data-pipeline/caids/export_vcfs.py:68
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