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rtracklayer

This is thereleased version of rtracklayer; for the devel version, seertracklayer.

R interface to genome annotation files and the UCSC genome browser

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DOI: 10.18129/B9.bioc.rtracklayer


Bioconductor version: Release (3.22)

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 <lawremi at gmail.com>

Citation (from within R, entercitation("rtracklayer")):

Installation

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 appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rtracklayer")
rtracklayerPDFR Script
Reference ManualPDF
NEWSText
INSTALLText
LICENSEText

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsAnnotation,DataImport,Software,Visualization
Version1.70.0
In Bioconductor sinceBioC 2.2 (R-2.7) (17.5 years)
LicenseArtistic-2.0 + fileLICENSE
DependsR (>= 3.5), methods,GenomicRanges(>= 1.37.2)
ImportsXML (>= 1.98-0),BiocGenerics(>= 0.35.3),S4Vectors(>= 0.23.18),IRanges(>= 2.13.13),XVector(>= 0.19.7),Seqinfo,Biostrings(>= 2.77.2),curl,httr,Rsamtools(>= 1.31.2),GenomicAlignments(>= 1.15.6),BiocIO, tools,restfulr (>= 0.0.13)
System Requirements
URL
See More
SuggestsGenomeInfoDb,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 ToS4Vectors,IRanges,XVector
Enhances
Depends On MeBSgenome,CAGEfightR,CoverageView,CSSQ,ExCluster,geneXtendeR,GenomicFiles,groHMM,HelloRanges,IdeoViz,MethylSeekR,ORFhunteR,r3Cseq,StructuralVariantAnnotation,svaNUMT,svaRetro,EatonEtAlChIPseq,liftOver,sequencing, csawBook, OSCA.intro
Imports MeAnnotationHubData,annotatr,ATACseqQC,ATACseqTFEA,ballgown,bedbaser,BgeeCall,BindingSiteFinder,biscuiteer,BiSeq,BSgenomeForge,CAGEr,casper,CexoR,chipenrich,ChIPpeakAnno,ChIPseeker,ChromHeatMap,ChromSCape,circRNAprofiler,cliProfiler,CNEr,consensusSeekeR,conumee,crisprDesign,crupR,derfinder,DEScan2,diffHic,diffUTR,DMCFB,DMCHMM,dmrseq,DuplexDiscovereR,easylift,ELMER,enhancerHomologSearch,ensembldb,EpiCompare,epidecodeR,epigraHMM,epimutacions,esATAC,extraChIPs,fcScan,FindIT2,FLAMES,geneAttribution,genomation,GenomicFeatures,GenomicInteractions,GenomicPlot,ggbio,gmapR,gmoviz,goseq,GOTHiC,GreyListChIP,gVenn,Gviz,HicAggR,HiCPotts,hicVennDiagram,HiTC,icetea,igvR,INSPEcT,IsoformSwitchAnalyzeR,karyoploteR,m6Aboost,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,PMScanR,pram,primirTSS,proBAMr,PureCN,qsea,QuasR,raer,RCAS,recount,recount3,recoup,regioneR,REMP,RiboCrypt,RiboProfiling,ribosomeProfilingQC,rifi,rifiComparative,rmspc,RNAmodR,roar,scanMiRApp,scDblFinder,scPipe,scRNAseqApp,scruff,seqCAT,seqsetvis,sevenC,SGSeq,shinyepico,signeR,SigsPack,sitadela,SOMNiBUS,SpliceWiz,srnadiff,STADyUM,TEKRABber,TENET,TFBSTools,tidyCoverage,trackViewer,transcriptR,TRESS,tRNAscanImport,txcutr,txdbmaker,VariantAnnotation,VariantTools,wavClusteR,wiggleplotr,GenomicState,chipenrich.data,DMRcatedata,geneLenDataBase,NxtIRFdata,raerdata,spatialLIBD,seqpac, OSTA,crispRdesignR,GALLO,GencoDymo2,locuszoomr,PlasmaMutationDetector,tepr
Suggests Mealabaster.files,AnnotationHub,autonomics,BiocFileCache,biovizBase,BREW3R.r,bsseq,cicero,compEpiTools,CrispRVariants,crisprViz,DAMEfinder,DiffBind,DMRcaller,eisaR,epistack,epivizrChart,epivizrData,FRASER,G4SNVHunter,geneXtendeR,GenomicAlignments,GenomicDistributions,GenomicInteractionNodes,gwascat,HiCExperiment,HiContacts,igvShiny,InPAS,interactiveDisplay,linkSet,megadepth,methylumi,miRBaseConverter,motifTestR,MutationalPatterns,NanoMethViz,OrganismDbi,peakCombiner,PICB,pipeFrame,plotgardener,plyinteractions,pqsfinder,ProteoDisco,RcisTarget,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,RnBeads,RSVSim,similaRpeak,syntenet,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,inDAGO,Rgff,Seurat,Signac
Links To Me
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Packagertracklayer_1.70.0.tar.gz
Windows Binary (x86_64) rtracklayer_1.70.0.zip
macOS Binary (x86_64)rtracklayer_1.70.0.tgz
macOS Binary (arm64)rtracklayer_1.70.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/rtracklayer
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/rtracklayer
Bioc Package Browserhttps://code.bioconductor.org/browse/rtracklayer/
Package Short Urlhttps://bioconductor.org/packages/rtracklayer/
Package Downloads ReportDownload Stats
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