rtracklayer

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see rtracklayer.

R interface to genome annotation files and the UCSC genome browser

DOI: 10.18129/B9.bioc.rtracklayer

Bioconductor version: 3.14

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 "4.1") 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 1.54.0

In Bioconductor since BioC 2.2 (R-2.7) (16 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)

System Requirements

URL

See More

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 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 ALPS, AnnotationHubData, annotatr, APAlyzer, ASpediaFI, ATACseqQC, ballgown, BgeeCall, BindingSiteFinder, biscuiteer, BiSeq, branchpointer, BSgenome, CAGEr, casper, CexoR, ChIPanalyser, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, chromswitch, circRNAprofiler, cliProfiler, CNEr, coMET, compartmap, consensusSeekeR, contiBAIT, conumee, customProDB, dasper, DeepBlueR, derfinder, DEScan2, diffHic, diffloop, diffUTR, DMCFB, DMCHMM, DMRcatedata, dmrseq, ELMER, ENCODExplorer, enhancerHomologSearch, enrichTF, ensembldb, epidecodeR, epigraHMM, erma, esATAC, exomePeak2, fcScan, FindIT2, 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, MACPET, MADSEQ, maser, MEDIPS, metagene, metagene2, metaseqR2, methrix, methylKit, motifbreakR, MotifDb, multicrispr, MungeSumstats, NADfinder, nearBynding, NoRCE, normr, NxtIRFcore, NxtIRFdata, ODER, OMICsPCA, ORFik, PAST, periodicDNA, plyranges, pram, primirTSS, proBAMr, profileplyr, PureCN, qsea, QuasR, RCAS, recount, recount3, recoup, regioneR, REMP, Repitools, RGMQL, RiboProfiling, ribosomeProfilingQC, RIPAT, RLSeq, rmspc, RNAmodR, roar, scanMiRApp, SCANVIS, scPipe, scruff, seqCAT, seqsetvis, sevenC, SGSeq, shinyepico, SigsPack, SingscoreAMLMutations, sitadela, soGGi, spatialLIBD, srnadiff, systemPipeRdata, TFBSTools, trackViewer, transcriptR, TRESS, tRNAscanImport, TSRchitect, txcutr, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr

Links To Me

Build Report Build Report

Package Archives

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

Source Package rtracklayer_1.54.0.tar.gz

Windows Binary rtracklayer_1.54.0.zip

macOS 10.13 (High Sierra) rtracklayer_1.54.0.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

Old Source Packages for BioC 3.14 Source Archive