Package: GenomicFeatures 1.63.1

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H. Pagès

GenomicFeatures: Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Authors:H. Pagès [aut, cre], M. Carlson [aut], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], D. Sarkar [aut], M. Lawrence [aut], V. Obenchain [aut], S. Arora [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], P. Shannon [ctb], L. Shepherd [ctb], D. Tenenbaum [ctb], D. Van Twisk [ctb]

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GenomicFeatures.pdf |GenomicFeatures.html✨
GenomicFeatures/json (API)
NEWS

# Install 'GenomicFeatures' in R:
install.packages('GenomicFeatures', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/genomicfeatures/issues

On BioConductor:GenomicFeatures-1.63.1(bioc 3.23)GenomicFeatures-1.62.0(bioc 3.22)

geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package

15.54 score 27 stars 350 packages 7.4k scripts 34k downloads 141 mentions 51 exports 66 dependencies

Last updated from:d92f2d08fd. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTotal timeArtifact
bioc-checksWARNING526
linux-devel-x86_64NOTE901
source / vignettesOK675
linux-release-x86_64NOTE918
macos-devel-arm64NOTE948
macos-release-arm64NOTE913
windows-develNOTE757
windows-releaseNOTE766
windows-oldrelNOTE758
wasm-releaseOK468

Exports:as.listasBEDasGFFcdscdsBycdsByOverlapscoverageByTranscriptdistanceexonicPartsexonsexonsByexonsByOverlapsextendExonsIntoIntronsextractTranscriptSeqsextractUpstreamSeqsfeaturesfiveUTRsByTranscriptgenesgetPromoterSeqgetTerminatorSeqid2nameintronicPartsintronsByTranscriptisActiveSeqisActiveSeq<-mapFromTranscriptsmapIdsToRangesmapRangesToIdsmapToTranscriptsorganismpcoverageByTranscriptpmapFromTranscriptspmapToTranscriptspromotersproteinToGenomeseqinfoseqlevels<-seqlevels0showterminatorsthreeUTRsByTranscripttidyExonstidyIntronstidyTranscriptstranscriptLengthstranscriptLocs2refLocstranscriptstranscriptsBytranscriptsByOverlapstranscriptWidthstRNAs

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLXVectoryaml

Obtaining and Utilizing TxDb Objects

Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan

Rendered fromGenomicFeatures.Rmdusingknitr::rmarkdownon Feb 03 2026.

Last update: 2024-03-12
Started: 2022-01-21

Readme and manuals

Help Manual

Help pageTopics
Coerce to file format structuresasBED,TxDb-method asGFF,TxDb-method
Compute coverage by transcript (or CDS) of a set of rangescoverageByTranscript pcoverageByTranscript
Extract non-overlapping exonic or intronic parts from a TxDb-like objectexonicParts intronicParts tidyExons tidyIntrons tidyTranscripts
Extend exons by a given number of bases into their adjacent intronsextendExonsIntoIntrons
Extract transcript (or CDS) sequences from chromosome sequencesextractTranscriptSeqs extractTranscriptSeqs,ANY-method extractTranscriptSeqs,DNAString-method
Extract sequences upstream of a set of genes or transcriptsextractUpstreamSeqs extractUpstreamSeqs,GenomicRanges-method extractUpstreamSeqs,GRangesList-method extractUpstreamSeqs,TxDb-method
FeatureDb objectsclass:FeatureDb FeatureDb FeatureDb-class
Extract simple features from a FeatureDb objectfeatures features,FeatureDb-method
Get gene promoter or terminator sequencesgetPromoterSeq getPromoterSeq,GRanges-method getPromoterSeq,GRangesList-method getTerminatorSeq getTerminatorSeq,GRanges-method getTerminatorSeq,GRangesList-method
Map internal ids to external names for a given feature typeid2name
Map IDs to Genomic RangesmapIdsToRanges mapIdsToRanges,TxDb-method
Map Genomic Ranges to IDsmapRangesToIds mapRangesToIds,TxDb-method
Map range coordinates between transcripts and genome spacecoordinate-mapping coordinate-mapping-methods mapFromTranscripts mapFromTranscripts,GenomicRanges,GenomicRanges-method mapFromTranscripts,GenomicRanges,GRangesList-method mapToTranscripts mapToTranscripts,ANY,TxDb-method mapToTranscripts,GenomicRanges,GenomicRanges-method mapToTranscripts,GenomicRanges,GRangesList-method pmapFromTranscripts pmapFromTranscripts,GenomicRanges,GenomicRanges-method pmapFromTranscripts,GenomicRanges,GRangesList-method pmapFromTranscripts,IntegerRanges,GenomicRanges-method pmapFromTranscripts,IntegerRanges,GRangesList-method pmapToTranscripts pmapToTranscripts,GenomicRanges,GenomicRanges-method pmapToTranscripts,GenomicRanges,GRangesList-method pmapToTranscripts,GRangesList,GRangesList-method
Finding the nearest genomic range neighbor in a TxDbdistance,GenomicRanges,TxDb-method nearest-methods
Map protein-relative coordinates to genomic coordinatesproteinToGenome proteinToGenome,ANY-method proteinToGenome,GRangesList-method
Using the "select" interface on TxDb objectscolumns,TxDb-method keys,TxDb-method keytypes,TxDb-method select,TxDb-method select-methods
Extract the transcript lengths (and other metrics) from a TxDb objecttranscriptLengths
Converting transcript-based locations into reference-based locationstranscriptLocs2refLocs transcriptWidths
Extract genomic features from a TxDb-like objectcds cds,TxDb-method exons exons,TxDb-method genes genes,TxDb-method promoters promoters,TxDb-method terminators terminators,TxDb-method transcripts transcripts,TxDb-method
Extract and group genomic features of a given type from a TxDb-like objectcdsBy cdsBy,TxDb-method exonsBy exonsBy,TxDb-method fiveUTRsByTranscript fiveUTRsByTranscript,TxDb-method intronsByTranscript intronsByTranscript,TxDb-method threeUTRsByTranscript threeUTRsByTranscript,TxDb-method transcriptsBy transcriptsBy,TxDb-method
Extract genomic features from a TxDb-like object based on their genomic locationcdsByOverlaps cdsByOverlaps,TxDb-method exonsByOverlaps exonsByOverlaps,TxDb-method transcriptsByOverlaps transcriptsByOverlaps,TxDb-method
Extract tRNA genomic ranges from an objecttRNAs tRNAs,TxDb-method
TxDb objectsas.list,TxDb-method class:TxDb isActiveSeq isActiveSeq,TxDb-method isActiveSeq<- isActiveSeq<-,TxDb-method organism,TxDb-method saveRDS,TxDb-method seqinfo,TxDb-method seqlevels0,TxDb-method seqlevels<-,TxDb-method show,TxDb-method TxDb TxDb-class
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