Package: GenomicFeatures 1.59.1

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:M. Carlson [aut], H. Pagès [aut, cre], 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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NEWS

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

Peer review:

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

On BioConductor:GenomicFeatures-1.59.0(bioc 3.21)GenomicFeatures-1.58.0(bioc 3.20)

geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package

15.39 score 26 stars 340 packages 5.3k scripts 34k downloads 141 mentions 71 exports 68 dependencies

Last updated 14 days agofrom:2d2ddd62a1. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winWARNINGNov 08 2024
R-4.5-linuxWARNINGNov 08 2024
R-4.4-winWARNINGNov 08 2024
R-4.4-macNOTENov 08 2024
R-4.3-winWARNINGNov 08 2024
R-4.3-macNOTENov 08 2024

Exports:as.listasBEDasGFFbrowseUCSCtrackcdscdsBycdsByOverlapscoverageByTranscriptdistanceexonicPartsexonsexonsByexonsByOverlapsextendExonsIntoIntronsextractTranscriptSeqsextractUpstreamSeqsfeaturesfiveUTRsByTranscriptgenesgetChromInfoFromBiomartgetPromoterSeqgetTerminatorSeqid2nameintronicPartsintronsByTranscriptisActiveSeqisActiveSeq<-makeFDbPackageFromUCSCmakeFeatureDbFromUCSCmakePackageNamemakeTxDbmakeTxDbFromBiomartmakeTxDbFromEnsemblmakeTxDbFromGFFmakeTxDbFromGRangesmakeTxDbFromUCSCmakeTxDbPackagemakeTxDbPackageFromBiomartmakeTxDbPackageFromUCSCmapFromTranscriptsmapIdsToRangesmapRangesToIdsmapToTranscriptsmicroRNAsorganismpcoverageByTranscriptpmapFromTranscriptspmapToTranscriptspromotersproteinToGenomeseqinfoseqlevels<-seqlevels0showsupportedMiRBaseBuildValuessupportedUCSCFeatureDbTablessupportedUCSCFeatureDbTrackssupportedUCSCtablesterminatorsthreeUTRsByTranscripttidyExonstidyIntronstidyTranscriptstranscriptLengthstranscriptLocs2refLocstranscriptstranscriptsBytranscriptsByOverlapstranscriptWidthstRNAsUCSCFeatureDbTableSchema

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc

Obtaining and Utilizing TxDb Objects

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

Rendered fromGenomicFeatures.Rmdusingknitr::rmarkdownon Nov 08 2024.

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
[Moved to txdbmaker] Make a FeatureDb object from annotations available at the UCSC Genome BrowsermakeFeatureDbFromUCSC supportedUCSCFeatureDbTables supportedUCSCFeatureDbTracks UCSCFeatureDbTableSchema
[Moved to txdbmaker] Make a TxDb object from user supplied annotationsmakeTxDb
[Moved to txdbmaker] Make a TxDb object from annotations available on a BioMart databasegetChromInfoFromBiomart makeTxDbFromBiomart
[Moved to txdbmaker] Make a TxDb object from an Ensembl databasemakeTxDbFromEnsembl
[Moved to txdbmaker] Make a TxDb object from annotations available as a GFF3 or GTF filemakeTxDbFromGFF
[Moved to txdbmaker] Make a TxDb object from a GRanges objectmakeTxDbFromGRanges
[Moved to txdbmaker] Make a TxDb object from annotations available at the UCSC Genome BrowserbrowseUCSCtrack makeTxDbFromUCSC supportedUCSCtables
[Moved to txdbmaker] Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.makeFDbPackageFromUCSC makePackageName makeTxDbPackage makeTxDbPackageFromBiomart makeTxDbPackageFromUCSC supportedMiRBaseBuildValues
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
Extract microRNA or tRNA genomic ranges from an objectmicroRNAs microRNAs,TxDb-method tRNAs tRNAs,TxDb-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
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