rtracklayer
R interface to genome annotation files and the UCSC genome browser
Bioconductor version: 3.23 · Package version: 1.72.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rtracklayer")Details
| Maintainer | Michael Lawrence <lawremi@gmail.com> |
| Author | Michael Lawrence, Vince Carey, Robert Gentleman |
| License | Artistic-2.0 + file LICENSE |
| Downloads rank | 24920 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataImport, Software, Visualization |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | rtracklayer_1.72.0.tar.gz |
| Windows binary (x86_64) | rtracklayer_1.72.0.zip |
| macOS binary (arm64) | rtracklayer_1.72.0.tgz |
| macOS binary (x86_64) | rtracklayer_1.72.0.tgz |
Dependencies
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)
LinkingTo: S4Vectors, IRanges, XVector
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
Reverse dependencies
Depends On Me (20): BSgenome, CAGEfightR, CoverageView, CSSQ, cummeRbund, EatonEtAlChIPseq, ExCluster, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, liftOver, MethylSeekR, ORFhunteR, r3Cseq, sequencing, StructuralVariantAnnotation, svaNUMT, svaRetro
Imports Me (182): AnnotationHubData, annotatr, APAlyzer, ATACseqQC, ATACseqTFEA, ballgown, bedbaser, BgeeCall, BindingSiteFinder, biscuiteer, BiSeq, branchpointer, BSgenomeForge, CAGEr, casper, CexoR, ChIPanalyser, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, circRNAprofiler, cliProfiler, CNEr, CNVScope, consensusSeekeR, conumee, crisprDesign, crispRdesignR, crupR, customProDB, damidBind, derfinder, DEScan2, diffHic, diffUTR, DMCFB, DMCHMM, DMRcatedata, dmrseq, DOTSeq, DuplexDiscovereR, easylift, ELMER, enhancerHomologSearch, ensembldb, EpiCompare, epidecodeR, epigraHMM, epimutacions, epiRomics, epiSeeker, esATAC, extraChIPs, factR, fcScan, FindIT2, FLAMES, GALLO, GencoDymo2, geneAttribution, geneLenDataBase, GeneStructureTools, genomation, GenomicFeatures, GenomicInteractions, GenomicPlot, GenomicState, ggbio, gmapR, gmoviz, goseq, GOTHiC, GreyListChIP, gVenn, Gviz, HicAggR, HiCDCPlus, HiCPotts, hicVennDiagram, HiTC, icetea, igvR, INSPEcT, InTAD, IsoformSwitchAnalyzeR, karyoploteR, locuszoomr, m6Aboost, magpie, maser, MEDIPS, metagene2, metaseqR2, methodical, methrix, methylKit, mist, mobileRNA, Moonlight2R, motifbreakR, MotifDb, MotifPeeker, multicrispr, MungeSumstats, NADfinder, NoRCE, normr, NxtIRFdata, ocrRBBR, OGRE, OMICsPCA, ORFik, PAST, periodicDNA, PlasmaMutationDetector, plyranges, PMScanR, PopPsiSeqR, pram, primirTSS, proBAMr, profileplyr, PureCN, qsea, QuasR, raer, raerdata, RCAS, recount, recount3, recoup, regioneR, REMP, RiboCrypt, RiboProfiling, ribosomeProfilingQC, rifi, rifiComparative, rmspc, RNAmodR, roar, scanMiRApp, SCANVIS, scDblFinder, scPipe, scRNAseqApp, scruff, seqCAT, seqpac, seqsetvis, sevenC, SGSeq, shinyepico, signeR, SigsPack, sitadela, SMTrackR, soGGi, SOMNiBUS, spatialLIBD, SpliceImpactR, SpliceWiz, srnadiff, STADyUM, TEKRABber, TENET, tepr, TFBSTools, tidyCoverage, trackViewer, transcriptR, TRESS, tRNAscanImport, txcutr, txdbmaker, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr
Suggests Me (79): alabaster.files, annoLinker, AnnotationHub, autonomics, BiocFileCache, biocohort, biovizBase, BREW3R.r, bsseq, chipseqDB, cicero, compEpiTools, CrispRVariants, crisprViz, DAMEfinder, DiffBind, DMRcaller, eisaR, epistack, EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3, epivizrChart, epivizrData, excluderanges, FDb.FANTOM4.promoters.hg19, fourDNData, FRASER, G4SNVHunter, GenomicAlignments, GenomicDistributions, GenomicInteractionNodes, GeuvadisTranscriptExpr, gkmSVM, GOaGO, gwascat, HiCExperiment, HiContacts, igvShiny, inDAGO, InPAS, linkSet, lncRna, megadepth, methylumi, miRBaseConverter, motifTestR, MutationalPatterns, NanoMethViz, nanotubes, OrganismDbi, PasillaTranscriptExpr, peakCombiner, PICB, pipeFrame, plotgardener, plyinteractions, pqsfinder, ProteoDisco, R453Plus1Toolbox, RcisTarget, Rgff, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, RSVSim, Seurat, Signac, similaRpeak, syntenet, systemPipeR, systemPipeRdata, TAPseq, TCGAutils, transmogR, triplex, tRNAdbImport, TVTB, xcore