To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

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

GenomicRanges

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges.

Representation and manipulation of genomic intervals

Bioconductor version: 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:// URLs are not supported
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	1.20.8
In Bioconductor since	BioC 2.6 (R-2.11) (6 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.6.6), 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_1.20.8.tar.gz
Windows Binary	GenomicRanges_1.20.8.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GenomicRanges_1.20.8.tgz
Mac OS X 10.9 (Mavericks)	GenomicRanges_1.20.8.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

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