rtracklayer

R interface to genome annotation files and the UCSC genome browser

Bioconductor version: Release (3.20)

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>

Citation (from within R, enter citation("rtracklayer")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

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

browseVignettes("rtracklayer")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, Software, Visualization
Version	1.66.0
In Bioconductor since	BioC 2.2 (R-2.7) (16.5 years)
License	Artistic-2.0 + file LICENSE
Depends	R (>= 3.5.0), 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, curl, httr, Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13)
System Requirements
URL

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, HelloRanges, IdeoViz, MethylSeekR, ORFhunteR, r3Cseq, StructuralVariantAnnotation, svaNUMT, svaRetro, EatonEtAlChIPseq, liftOver, sequencing, csawBook, OSCA.intro
Imports Me	AnnotationHubData, annotatr, APAlyzer, ATACseqQC, ATACseqTFEA, ballgown, BgeeCall, BindingSiteFinder, biscuiteer, BiSeq, branchpointer, BSgenomeForge, CAGEr, casper, CexoR, chipenrich, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, circRNAprofiler, cliProfiler, CNEr, consensusSeekeR, conumee, crisprDesign, 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, methrix, methylKit, mobileRNA, Moonlight2R, motifbreakR, MotifDb, 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, RNAmodR, roar, scanMiRApp, scDblFinder, scPipe, scRNAseqApp, scruff, seqCAT, seqsetvis, sevenC, SGSeq, shinyepico, signeR, SigsPack, sitadela, soGGi, SpliceWiz, syntenet, TEKRABber, TFBSTools, tidyCoverage, trackViewer, transcriptR, TRESS, tRNAscanImport, txcutr, txdbmaker, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr, GenomicState, chipenrich.data, DMRcatedata, geneLenDataBase, NxtIRFdata, raerdata, spatialLIBD, seqpac, SingscoreAMLMutations, crispRdesignR, GALLO, geneHapR, kibior, locuszoomr, PlasmaMutationDetector, PlasmaMutationDetector2, valr
Suggests Me	alabaster.files, AnnotationHub, autonomics, BiocFileCache, biovizBase, BREW3R.r, bsseq, cicero, CINdex, compEpiTools, CrispRVariants, crisprViz, DAMEfinder, DiffBind, eisaR, epistack, epivizrChart, epivizrData, FRASER, geneXtendeR, GenomicAlignments, GenomicDistributions, GenomicInteractionNodes, GenomicRanges, gwascat, HiCExperiment, HiContacts, igvShiny, InPAS, interactiveDisplay, megadepth, methylumi, miRBaseConverter, motifTestR, MutationalPatterns, NanoMethViz, OrganismDbi, 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, MOCHA, Rgff, RTIGER, Seurat, Signac
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	rtracklayer_1.66.0.tar.gz
Windows Binary (x86_64)	rtracklayer_1.66.0.zip
macOS Binary (x86_64)	rtracklayer_1.66.0.tgz
macOS Binary (arm64)	rtracklayer_1.66.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rtracklayer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rtracklayer
Bioc Package Browser	https://code.bioconductor.org/browse/rtracklayer/
Package Short Url	https://bioconductor.org/packages/rtracklayer/
Package Downloads Report	Download Stats