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Bioconductor - rtracklayer (development version)

rtracklayer

This is the development version of rtracklayer; for the stable release version, see rtracklayer.

R interface to genome annotation files and the UCSC genome browser

Bioconductor version: Development (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 <michafla at gene.com>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Details biocViews Annotation, DataImport, Software, Visualization Version 1.69.1 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), 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 Suggests GenomeInfoDb, 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, circRNAprofiler, cliProfiler, consensusSeekeR, conumee, crisprDesign, crupR, customProDB, derfinder, DEScan2, diffHic, diffUTR, DMCFB, DMCHMM, dmrseq, DuplexDiscovereR, easylift, ELMER, enhancerHomologSearch, ensembldb, EpiCompare, epidecodeR, epigraHMM, epimutacions, 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, 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, RiboCrypt, 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, seqpac, crispRdesignR, GALLO, GencoDymo2, geneHapR, inDAGO, locuszoomr, PlasmaMutationDetector, tepr Suggests Me alabaster.files, AnnotationHub, autonomics, BiocFileCache, biovizBase, BREW3R.r, bsseq, cicero, CINdex, 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, pipeFrame, plotgardener, plyinteractions, pqsfinder, ProteoDisco, R453Plus1Toolbox, RcisTarget, 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 Package Archives

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