To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

In most cases, you don't need to download the package archive at all.

GenomicRanges

 

Representation and manipulation of genomic intervals

Bioconductor version: Release (3.1)

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals. Specialized containers for representing and manipulating short alignments against a reference genome are defined in the GenomicAlignments package.

Author: P. Aboyoun, H. Pages and M. Lawrence

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GenomicRanges")):

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicRanges")

 

PDF R Script A quick introduction to GRanges and GRangesList objects
PDF R Script An Introduction to GenomicRanges
PDF R Script Extending GenomicRanges
PDF R Script GenomicRanges HOWTOs
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.20.6
In Bioconductor since BioC 2.6 (R-2.11) (5.5 years)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.5.14), IRanges(>= 2.2.4), GenomeInfoDb(>= 1.1.20)
Imports utils, stats, XVector
LinkingTo S4Vectors, IRanges
Suggests AnnotationDbi(>= 1.21.1), AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, Biobase, BiocStyle, Biostrings(>= 2.25.3), DESeq, DEXSeq, GenomicAlignments, GenomicFeatures, KEGG.db, KEGGgraph, RUnit, Rsamtools(>= 1.13.53), TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, annotate, digest, edgeR, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, rtracklayer
SystemRequirements
Enhances
URL
Depends On Me airway, ALDEx2, AllelicImbalance, annmap, Basic4Cseq, baySeq, biomvRCNS, BiSeq, BSgenome, bsseq, bumphunter, CAFE, casper, cheung2010, chimera, ChIPpeakAnno, ChIPQC, chipseq, cleanUpdTSeq, cn.mops, cnvGSA, compEpiTools, CSAR, csaw, DASiR, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DMRcaller, DMRforPairs, DREAM4, dsQTL, EatonEtAlChIPseq, ensembldb, ensemblVEP, epigenomix, epivizr, exomeCopy, fastseg, fission, FourCSeq, geneRxCluster, genomes, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicTuples, genoset, GenoView, geuvPack, geuvStore, ggtut, gmapR, GOTHiC, GreyListChIP, groHMM, Gviz, hiAnnotator, HiTC, htSeqTools, IdeoViz, InPAS, intansv, MBASED, metagene, methyAnalysis, methylPipe, minfi, MMDiff, OmicCircos, parathyroidSE, PING, podkat, QuasR, r3Cseq, R453Plus1Toolbox, Rariant, Rcade, regioneR, rfPred, rGREAT, riboSeqR, RIPSeeker, RnBeads, RnBeads.hg19, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, segmentSeq, seqbias, SGSeq, SigFuge, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomatiCA, SomaticSignatures, trackViewer, TransView, VanillaICE, VariantAnnotation, VariantTools, vtpnet, wavClusteR, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me ArrayExpressHTS, ballgown, bamsignals, beadarray, BEAT, biovizBase, BiSeq, BSgenome, BubbleTree, CAGEr, CexoR, ChAMP, chipenrich, chipenrich.data, ChIPseeker, chipseq, ChIPseqR, chromDraw, CNEr, coMET, conumee, copynumber, CopywriteR, COSMIC.67, CoverageView, customProDB, derfinder, derfinderPlot, DOQTL, easyRNASeq, EnrichmentBrowser, flipflop, FourCSeq, FunciSNP, genomation, GenomicAlignments, GenomicInteractions, GGBase, ggbio, GGtools, GoogleGenomics, gQTLBase, gQTLstats, gwascat, h5vc, hiReadsProcessor, HTSeqGenie, IVAS, leeBamViews, lumi, M3D, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, MEDIPS, methyAnalysis, MethylSeekR, methylumi, MinimumDistance, MMDiff, NarrowPeaks, nucleR, oligoClasses, Pbase, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons7way.UCSC.hg38, PICS, prebs, proBAMr, Pviz, pwOmics, qpgraph, R3CPET, regioneR, regionReport, Repitools, rgsepd, RNAprobR, rnaSeqMap, roar, seq2pathway, SeqArray, seqPattern, seqplots, SeqVarTools, ShortRead, simulatorZ, SNPchip, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, soGGi, SomatiCA, SomaticCancerAlterations, spliceR, SplicingGraphs, SVM2CRM, systemPipeR, TFBSTools, ToPASeq, tracktables, triplex, VariantFiltering, waveTiling, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me AnnotationHub, BeadArrayUseCases, BiocGenerics, BiocParallel, cummeRbund, GenomeInfoDb, gtrellis, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, NGScopy, SeqGSEA, STAN
Build Report  

Package Archives

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

Package Source GenomicRanges_1.20.6.tar.gz
Windows Binary GenomicRanges_1.20.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicRanges_1.20.6.tgz
Mac OS X 10.9 (Mavericks) GenomicRanges_1.20.6.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomicRanges/tree/release-3.1
Package Short Url http://bioconductor.org/packages/GenomicRanges/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center