This is the released version of rtracklayer; for the devel version, seertracklayer .
Bioconductor version: Release (3.21)
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Author: Michael Lawrence, Vince Carey, Robert Gentleman
Maintainer: Michael Lawrence
Citation (from within R, enter citation("rtracklayer")):
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rtracklayer")
For older versions of R, please refer to the appropriate Bioconductor release .
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rtracklayer")
biocViews
Annotation , DataImport , Software , Visualization
Version
1.68.0
In Bioconductor since
BioC 2.2 (R-2.7) (17 years)
License
Artistic-2.0 + file LICENSE
Depends
R (>= 3.5), methods, GenomicRanges (>= 1.37.2)
Imports
XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), curl , httr , Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO , tools, restfulr (>= 0.0.13)
System Requirements
URL
See More
Suggests
BSgenome (>= 1.33.4), humanStemCell , microRNA (>= 1.1.1), genefilter , limma , org.Hs.eg.db , hgu133plus2.db , GenomicFeatures , BSgenome.Hsapiens.UCSC.hg19 , TxDb.Hsapiens.UCSC.hg19.knownGene , RUnit
Linking To
S4Vectors , IRanges , XVector
Enhances
Depends On Me
BSgenome , CAGEfightR , CoverageView , CSSQ , cummeRbund , ExCluster , geneXtendeR , GenomicFiles , groHMM , HelloRanges , IdeoViz , MethylSeekR , ORFhunteR , r3Cseq , StructuralVariantAnnotation , svaNUMT , svaRetro , EatonEtAlChIPseq , liftOver , sequencing , csawBook, OSCA.intro
Imports Me
AnnotationHubData , annotatr , APAlyzer , ATACseqQC , ATACseqTFEA , ballgown , bedbaser , BgeeCall , BindingSiteFinder , biscuiteer , BiSeq , branchpointer , BSgenomeForge , CAGEr , casper , CexoR , chipenrich , ChIPpeakAnno , ChIPseeker , ChromHeatMap , ChromSCape , circRNAprofiler , cliProfiler , CNEr , consensusSeekeR , conumee , crisprDesign , crupR , customProDB , derfinder , DEScan2 , diffHic , diffUTR , DMCFB , DMCHMM , dmrseq , DuplexDiscovereR , easylift , ELMER , enhancerHomologSearch , ensembldb , EpiCompare , epidecodeR , epigraHMM , epimutacions , erma , esATAC , extraChIPs , factR , fcScan , FindIT2 , FLAMES , geneAttribution , genomation , GenomicFeatures , GenomicInteractions , GenomicPlot , ggbio , gmapR , gmoviz , goseq , GOTHiC , GreyListChIP , Gviz , hiAnnotator , HicAggR , hicVennDiagram , HiTC , icetea , igvR , INSPEcT , IsoformSwitchAnalyzeR , karyoploteR , m6Aboost , MADSEQ , magpie , maser , MEDIPS , metagene2 , metaseqR2 , methodical , methrix , methylKit , mist , mobileRNA , Moonlight2R , motifbreakR , MotifDb , MotifPeeker , multicrispr , MungeSumstats , NADfinder , nearBynding , normr , OGRE , OMICsPCA , ORFik , PAST , periodicDNA , plyranges , pram , primirTSS , proBAMr , profileplyr , PureCN , qsea , QuasR , raer , RCAS , recount , recount3 , recoup , regioneR , REMP , Repitools , RiboProfiling , ribosomeProfilingQC , rifi , rifiComparative , rmspc , RNAmodR , roar , scanMiRApp , scDblFinder , scPipe , scRNAseqApp , scruff , seqCAT , seqsetvis , sevenC , SGSeq , shinyepico , signeR , SigsPack , sitadela , soGGi , SOMNiBUS , SpliceWiz , srnadiff , syntenet , TEKRABber , TENET , TFBSTools , tidyCoverage , trackViewer , transcriptR , TRESS , tRNAscanImport , txcutr , txdbmaker , VariantAnnotation , VariantTools , wavClusteR , wiggleplotr , GenomicState , chipenrich.data , DMRcatedata , geneLenDataBase , NxtIRFdata , raerdata , spatialLIBD , SingscoreAMLMutations , crispRdesignR , GALLO , geneHapR , locuszoomr , PlasmaMutationDetector , tepr
Suggests Me
alabaster.files , AnnotationHub , autonomics , BiocFileCache , biovizBase , BREW3R.r , bsseq , cicero , CINdex , compEpiTools , CrispRVariants , crisprViz , DAMEfinder , DiffBind , eisaR , epistack , epivizrChart , epivizrData , FRASER , G4SNVHunter , geneXtendeR , GenomicAlignments , GenomicDistributions , GenomicInteractionNodes , GenomicRanges , gwascat , HiCExperiment , HiContacts , igvShiny , InPAS , interactiveDisplay , megadepth , methylumi , miRBaseConverter , motifTestR , MutationalPatterns , NanoMethViz , OrganismDbi , PICB , PICS , PING , pipeFrame , plotgardener , plyinteractions , pqsfinder , ProteoDisco , R453Plus1Toolbox , RcisTarget , rGADEM , RNAmodR.AlkAnilineSeq , RNAmodR.ML , RNAmodR.RiboMethSeq , RnBeads , RSVSim , similaRpeak , systemPipeR , TAPseq , TCGAutils , transmogR , triplex , tRNAdbImport , TVTB , xcore , EpiTxDb.Hs.hg38 , EpiTxDb.Sc.sacCer3 , excluderanges , FDb.FANTOM4.promoters.hg19 , fourDNData , GeuvadisTranscriptExpr , nanotubes , PasillaTranscriptExpr , systemPipeRdata , chipseqDB , gkmSVM , Rgff , RTIGER , Seurat , Signac
Links To Me
Build Report
Build Report
Follow Installation instructions to use this package in your R session.