Package: GenomicFeatures 1.57.0
H. Pagès
GenomicFeatures: Conveniently import and query gene models
A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.
Authors:
GenomicFeatures_1.57.0.tar.gz
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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-1.57.0(bioc 3.20)GenomicFeatures-1.56.0(bioc 3.19)
Last updated 2 months agofrom:9d8d2d904a
Exports:as.listasBEDasGFFbrowseUCSCtrackcdscdsBycdsByOverlapscoverageByTranscriptdistanceexonicPartsexonsexonsByexonsByOverlapsextendExonsIntoIntronsextractTranscriptSeqsextractUpstreamSeqsfeaturesfiveUTRsByTranscriptgenesgetChromInfoFromBiomartgetPromoterSeqgetTerminatorSeqid2nameintronicPartsintronsByTranscriptisActiveSeqisActiveSeq<-makeFDbPackageFromUCSCmakeFeatureDbFromUCSCmakePackageNamemakeTxDbmakeTxDbFromBiomartmakeTxDbFromEnsemblmakeTxDbFromGFFmakeTxDbFromGRangesmakeTxDbFromUCSCmakeTxDbPackagemakeTxDbPackageFromBiomartmakeTxDbPackageFromUCSCmapFromTranscriptsmapIdsToRangesmapRangesToIdsmapToTranscriptsmicroRNAsorganismpcoverageByTranscriptpmapFromTranscriptspmapToTranscriptspromotersproteinToGenomeseqinfoseqlevels<-seqlevels0showsupportedMiRBaseBuildValuessupportedUCSCFeatureDbTablessupportedUCSCFeatureDbTrackssupportedUCSCtablesterminatorsthreeUTRsByTranscripttidyExonstidyIntronstidyTranscriptstranscriptLengthstranscriptLocs2refLocstranscriptstranscriptsBytranscriptsByOverlapstranscriptWidthstRNAsUCSCFeatureDbTableSchema
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Coerce to file format structures | asBED,TxDb-method asGFF,TxDb-method |
| Compute coverage by transcript (or CDS) of a set of ranges | coverageByTranscript pcoverageByTranscript |
| Extract non-overlapping exonic or intronic parts from a TxDb-like object | exonicParts intronicParts tidyExons tidyIntrons tidyTranscripts |
| Extend exons by a given number of bases into their adjacent introns | extendExonsIntoIntrons |
| Extract transcript (or CDS) sequences from chromosome sequences | extractTranscriptSeqs extractTranscriptSeqs,ANY-method extractTranscriptSeqs,DNAString-method |
| Extract sequences upstream of a set of genes or transcripts | extractUpstreamSeqs extractUpstreamSeqs,GenomicRanges-method extractUpstreamSeqs,GRangesList-method extractUpstreamSeqs,TxDb-method |
| FeatureDb objects | class:FeatureDb FeatureDb FeatureDb-class |
| Extract simple features from a FeatureDb object | features features,FeatureDb-method |
| Get gene promoter or terminator sequences | getPromoterSeq getPromoterSeq,GRanges-method getPromoterSeq,GRangesList-method getTerminatorSeq getTerminatorSeq,GRanges-method getTerminatorSeq,GRangesList-method |
| Map internal ids to external names for a given feature type | id2name |
| [Moved to txdbmaker] Make a FeatureDb object from annotations available at the UCSC Genome Browser | makeFeatureDbFromUCSC supportedUCSCFeatureDbTables supportedUCSCFeatureDbTracks UCSCFeatureDbTableSchema |
| [Moved to txdbmaker] Make a TxDb object from user supplied annotations | makeTxDb |
| [Moved to txdbmaker] Make a TxDb object from annotations available on a BioMart database | getChromInfoFromBiomart makeTxDbFromBiomart |
| [Moved to txdbmaker] Make a TxDb object from an Ensembl database | makeTxDbFromEnsembl |
| [Moved to txdbmaker] Make a TxDb object from annotations available as a GFF3 or GTF file | makeTxDbFromGFF |
| [Moved to txdbmaker] Make a TxDb object from a GRanges object | makeTxDbFromGRanges |
| [Moved to txdbmaker] Make a TxDb object from annotations available at the UCSC Genome Browser | browseUCSCtrack 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 Ranges | mapIdsToRanges mapIdsToRanges,TxDb-method |
| Map Genomic Ranges to IDs | mapRangesToIds mapRangesToIds,TxDb-method |
| Map range coordinates between transcripts and genome space | coordinate-mapping 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 object | microRNAs microRNAs,TxDb-method tRNAs tRNAs,TxDb-method |
| Finding the nearest genomic range neighbor in a TxDb | distance,GenomicRanges,TxDb-method nearest-methods |
| Map protein-relative coordinates to genomic coordinates | proteinToGenome proteinToGenome,ANY-method proteinToGenome,GRangesList-method |
| Using the "select" interface on TxDb objects | columns,TxDb-method keys,TxDb-method keytypes,TxDb-method select,TxDb-method select-methods |
| Extract the transcript lengths (and other metrics) from a TxDb object | transcriptLengths |
| Converting transcript-based locations into reference-based locations | transcriptLocs2refLocs transcriptWidths |
| Extract genomic features from a TxDb-like object | cds 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 object | cdsBy 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 location | cdsByOverlaps cdsByOverlaps,TxDb-method exonsByOverlaps exonsByOverlaps,TxDb-method transcriptsByOverlaps transcriptsByOverlaps,TxDb-method |
| TxDb objects | as.list,TxDb-method class:TxDb isActiveSeq isActiveSeq,TxDb-method isActiveSeq<- isActiveSeq<-,TxDb-method organism,TxDb-method seqinfo,TxDb-method seqlevels0,TxDb-method seqlevels<-,TxDb-method show,TxDb-method TxDb TxDb-class |
