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rtracklayer

R interface to genome annotation files and the UCSC genome browser

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Annotation, DataImport, Software, Visualization
Version 1.60.0
In Bioconductor since BioC 2.2 (R-2.7) (15.5 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, RCurl (>= 1.4-2), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13)
Linking To 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
System Requirements
Enhances
URL
See More
Depends On Me BRGenomics, BSgenome, CAGEfightR, ChIPComp, CoverageView, CSSQ, cummeRbund, EatonEtAlChIPseq, ExCluster, geneXtendeR, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, liftOver, MethylSeekR, ORFhunteR, r3Cseq, sequencing, StructuralVariantAnnotation, svaNUMT, svaRetro
Imports Me AnnotationHubData, annotatr, APAlyzer, ASpediaFI, ATACseqQC, ballgown, BgeeCall, BindingSiteFinder, biscuiteer, BiSeq, branchpointer, BSgenome, BSgenomeForge, CAGEr, casper, CexoR, ChIPanalyser, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, chromswitch, circRNAprofiler, cliProfiler, CNEr, coMET, compartmap, consensusSeekeR, contiBAIT, conumee, crisprDesign, customProDB, dasper, DeepBlueR, derfinder, DEScan2, diffHic, diffUTR, DMCFB, DMCHMM, DMRcatedata, dmrseq, ELMER, enhancerHomologSearch, enrichTF, ensembldb, EpiCompare, epidecodeR, epigraHMM, epimutacions, erma, esATAC, exomePeak2, extraChIPs, factR, fcScan, FindIT2, FLAMES, 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, m6Aboost, MADSEQ, magpie, maser, MEDIPS, metagene, metagene2, metaseqR2, methrix, methylKit, motifbreakR, MotifDb, multicrispr, MungeSumstats, NADfinder, nearBynding, NoRCE, normr, NxtIRFcore, NxtIRFdata, ODER, OGRE, OMICsPCA, ORFik, PAST, periodicDNA, plyranges, pram, primirTSS, proBAMr, profileplyr, PureCN, qsea, QuasR, RCAS, recount, recount3, recoup, regioneR, REMP, Repitools, RGMQL, RiboProfiling, ribosomeProfilingQC, rifi, rifiComparative, RIPAT, RLSeq, rmspc, RNAmodR, roar, scanMiRApp, SCANVIS, scDblFinder, scPipe, scRNAseqApp, scruff, seqCAT, seqpac, seqsetvis, sevenC, SGSeq, shinyepico, signeR, SigsPack, SingscoreAMLMutations, sitadela, soGGi, spatialLIBD, SpliceWiz, srnadiff, syntenet, TFBSTools, trackViewer, transcriptR, TRESS, tRNAscanImport, txcutr, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr
Suggests Me alpine, AnnotationHub, autonomics, BiocFileCache, biovizBase, bsseq, chipseqDB, cicero, CINdex, compEpiTools, CrispRVariants, crisprViz, DAMEfinder, DiffBind, eisaR, epistack, EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3, epivizrChart, epivizrData, excluderanges, FDb.FANTOM4.promoters.hg19, fourDNData, geneXtendeR, GenomicAlignments, GenomicDistributions, GenomicInteractionNodes, GenomicRanges, GeuvadisTranscriptExpr, goseq, gwascat, HiCExperiment, HiContacts, InPAS, interactiveDisplay, megadepth, methylumi, miRBaseConverter, MutationalPatterns, NanoMethViz, nanotubes, OrganismDbi, PasillaTranscriptExpr, Pi, PICS, PING, pipeFrame, plotgardener, pqsfinder, ProteoDisco, R453Plus1Toolbox, RcisTarget, rGADEM, Ringo, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, RSVSim, similaRpeak, systemPipeR, systemPipeRdata, TAPseq, TCGAutils, triplex, tRNAdbImport, TVTB, xcore
Links To Me
Build Report  

Package Archives

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

Source Package rtracklayer_1.60.0.tar.gz
Windows Binary rtracklayer_1.60.0.zip
macOS Binary (x86_64) rtracklayer_1.60.0.tgz
macOS Binary (arm64) rtracklayer_1.60.0.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