rtracklayer

DOI: 10.18129/B9.bioc.rtracklayer    

R interface to genome annotation files and the UCSC genome browser

Bioconductor version: Release (3.13)

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 <michafla at gene.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rtracklayer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("rtracklayer")

 

PDF	R Script	rtracklayer
PDF		Reference Manual
Text		NEWS
Text		INSTALL
Text		LICENSE

Details

biocViews	Annotation, DataImport, Software, Visualization
Version	1.52.1
In Bioconductor since	BioC 2.2 (R-2.7) (13.5 years)
License	Artistic-2.0 + file LICENSE
Depends	R (>= 3.3), 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), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13)
LinkingTo	S4Vectors, IRanges, XVector
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
SystemRequirements
Enhances
URL
Depends On Me	BRGenomics, BSgenome, CAGEfightR, ChIPComp, ChIPSeqSpike, CoverageView, CSSQ, cummeRbund, EatonEtAlChIPseq, ExCluster, geneXtendeR, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, liftOver, MethylSeekR, ORFhunteR, r3Cseq, sequencing, StructuralVariantAnnotation
Imports Me	ALPS, AnnotationHubData, annotatr, APAlyzer, ASpediaFI, ATACseqQC, ballgown, BgeeCall, biscuiteer, BiSeq, branchpointer, BSgenome, CAGEr, casper, CexoR, ChIPanalyser, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, chromswitch, circRNAprofiler, CNEr, coMET, compartmap, CompGO, consensusSeekeR, contiBAIT, conumee, customProDB, DeepBlueR, derfinder, DEScan2, diffHic, diffloop, diffUTR, DMCFB, DMCHMM, DMRcatedata, dmrseq, ELMER, ENCODExplorer, enrichTF, ensembldb, epidecodeR, epigraHMM, erma, esATAC, exomePeak2, fcScan, genbankr, geneAttribution, geneLenDataBase, GeneStructureTools, genomation, GenomicFeatures, GenomicInteractions, GenomicState, genotypeeval, ggbio, gmapR, gmoviz, GOTHiC, GreyListChIP, Gviz, hiAnnotator, HiCDCPlus, HiTC, HTSeqGenie, icetea, igvR, INSPEcT, InTAD, IsoformSwitchAnalyzeR, karyoploteR, MACPET, MADSEQ, maser, MEDIPS, metagene, metagene2, metaseqR2, methrix, methyAnalysis, methylKit, motifbreakR, MotifDb, multicrispr, NADfinder, nanotatoR, nearBynding, NoRCE, normr, OMICsPCA, ORFik, PAST, periodicDNA, plyranges, pram, primirTSS, proBAMr, profileplyr, PureCN, qsea, QuasR, RCAS, recount, recount3, recoup, regioneR, REMP, Repitools, RGMQL, RiboProfiling, ribosomeProfilingQC, RIPAT, RNAmodR, RNAprobR, roar, SCANVIS, scPipe, scruff, seqCAT, seqplots, seqsetvis, sevenC, SGSeq, shinyepico, SigsPack, SingscoreAMLMutations, sitadela, soGGi, srnadiff, systemPipeRdata, TFBSTools, trackViewer, transcriptR, tRNAscanImport, TSRchitect, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr
Suggests Me	alpine, AnnotationHub, autonomics, BiocFileCache, biovizBase, bsseq, chipseqDB, cicero, CINdex, compEpiTools, CrispRVariants, DAMEfinder, dasper, dsQTL, eisaR, EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3, epivizrChart, epivizrData, FDb.FANTOM4.promoters.hg19, geneXtendeR, GenomicAlignments, GenomicDistributions, GenomicRanges, GeuvadisTranscriptExpr, goseq, gwascat, InPAS, interactiveDisplay, megadepth, methylumi, miRBaseConverter, MutationalPatterns, nanotubes, OrganismDbi, PasillaTranscriptExpr, Pi, PICS, PING, pipeFrame, pqsfinder, R453Plus1Toolbox, RcisTarget, rGADEM, Ringo, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, RSVSim, signeR, similaRpeak, spatialLIBD, SynExtend, TAPseq, TCGAutils, triplex, tRNAdbImport, TVTB
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rtracklayer_1.52.1.tar.gz
Windows Binary	rtracklayer_1.52.1.zip
macOS 10.13 (High Sierra)	rtracklayer_1.52.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rtracklayer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rtracklayer
Package Short Url	https://bioconductor.org/packages/rtracklayer/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive