rtracklayer
DOI:
10.18129/B9.bioc.rtracklayer
R interface to genome annotation files and the UCSC genome browser
Bioconductor version: Release (3.6)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")
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 |
1.38.3 |
In Bioconductor since |
BioC 2.2 (R-2.7) (10 years) |
License |
Artistic-2.0 + file LICENSE |
Depends |
R (>= 3.3), methods, GenomicRanges(>= 1.21.20) |
Imports |
XML (>= 1.98-0), BiocGenerics(>= 0.13.8), S4Vectors(>= 0.13.13), IRanges(>= 2.11.12), XVector(>= 0.9.4), GenomeInfoDb(>= 1.3.14), Biostrings(>= 2.43.7), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.17.8), GenomicAlignments(>= 1.5.4), tools |
LinkingTo |
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 |
SystemRequirements |
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Enhances |
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URL |
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Depends On Me |
BSgenome, ChIPComp, CoverageView, cummeRbund, EatonEtAlChIPseq, exomePeak, geneXtendeR, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, MethylSeekR, r3Cseq, regioneR, RIPSeeker, spliceR |
Imports Me |
AnnotationHubData, annotatr, ATACseqQC, ballgown, BiSeq, branchpointer, BSgenome, CAGEr, casper, CexoR, chipenrich, chipenrich.data, ChIPseeker, ChromHeatMap, chromswitch, CNEr, coMET, CompGO, consensusSeekeR, contiBAIT, conumee, customProDB, DeepBlueR, derfinder, diffloop, DMCHMM, ensembldb, erma, esATAC, FourCSeq, FunciSNP, FunciSNP.data, genbankr, geneAttribution, geneLenDataBase, genomation, GenomicFeatures, GenomicInteractions, genotypeeval, ggbio, GGtools, gmapR, GOTHiC, gQTLBase, GreyListChIP, Gviz, gwascat, hiAnnotator, HiTC, HTSeqGenie, IsoformSwitchAnalyzeR, karyoploteR, MADSEQ, MEDIPS, metagene, methyAnalysis, methylKit, motifbreakR, MotifDb, NADfinder, normr, Pbase, PGA, proBAMr, PureCN, qsea, QuasR, RCAS, recount, recoup, regioneR, Repitools, RiboProfiling, RNAprobR, roar, seqplots, SGSeq, soGGi, SVM2CRM, TFBSTools, trackViewer, transcriptR, TSRchitect, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr |
Suggests Me |
alpine, AnnotationHub, BiocFileCache, biovizBase, ChIPpeakAnno, CINdex, compEpiTools, CrispRVariants, dsQTL, ELMER, epivizrData, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, GeuvadisTranscriptExpr, goseq, InPAS, interactiveDisplay, metaseqR, methylumi, miRBaseConverter, MotIV, MutationalPatterns, NarrowPeaks, oneChannelGUI, OrganismDbi, PasillaTranscriptExpr, PICS, PING, pqsfinder, R453Plus1Toolbox, Ringo, rMAT, RnBeads, RSVSim, signeR, similaRpeak, triplex, TSSi, TVTB |
Build Report |
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