GenomicRanges

Representation and manipulation of genomic intervals

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GenomicRanges")

To cite this package in a publication, start R and enter:

    citation("GenomicRanges")

Documentation

PDF R Script An Introduction to GenomicRanges
PDF R Script GenomicRanges HOWTOs
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Genetics, Infrastructure, Sequencing, Software
Version 1.16.2
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.7.7), IRanges(>= 1.21.33), GenomeInfoDb(>= 0.99.17)
Imports methods, utils, stats, BiocGenerics, IRanges, XVector
Suggests AnnotationDbi(>= 1.21.1), AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, Biostrings(>= 2.25.3), Rsamtools(>= 1.13.53), GenomicAlignments, rtracklayer, KEGG.db, KEGGgraph, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, seqnames.db, org.Sc.sgd.db, VariantAnnotation, edgeR, DESeq, DEXSeq, pasilla, pasillaBamSubset, RUnit, digest, BiocStyle
System Requirements
URL
Depends On Me AllelicImbalance, annmap, Basic4Cseq, baySeq, biomvRCNS, BiSeq, BSgenome, bsseq, bumphunter, CAFE, casper, cheung2010, chimera, chipseq, cleanUpdTSeq, cn.mops, COPDSexualDimorphism, CSAR, DASiR, deepSNV, DESeq2, DEXSeq, DiffBind, DMRforPairs, DREAM4, dsQTL, EatonEtAlChIPseq, ensemblVEP, epigenomix, epivizr, exomeCopy, fastseg, geneRxCluster, genomes, GenomicAlignments, GenomicFeatures, genoset, ggtut, gmapR, GOTHiC, HiTC, htSeqTools, intansv, methyAnalysis, minfi, MMDiff, OmicCircos, parathyroidSE, PING, QuasR, r3Cseq, R453Plus1Toolbox, Rcade, rfPred, RIPSeeker, Rsamtools, rSFFreader, RSVSim, rtracklayer, segmentSeq, seqbias, 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, SomatiCA, SplicingGraphs, trackViewer, TransView, VariantAnnotation, VariantTools, vtpnet
Imports Me AnnotationHub, ArrayExpressHTS, beadarray, BEAT, biovizBase, BiSeq, BSgenome, CAGEr, CexoR, chipenrich, chipenrich.data, ChIPQC, ChIPseeker, chipseq, ChIPseqR, CNEr, copynumber, COSMIC.67, CoverageView, customProDB, DNaseR, easyRNASeq, flipflop, FunciSNP, GenomicAlignments, ggbio, GGtools, Gviz, gwascat, h5vc, HTSeqGenie, HTSFilter, leeBamViews, lumi, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MEDIPS, methyAnalysis, MethylSeekR, MinimumDistance, MMDiff, NarrowPeaks, nucleR, oligoClasses, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg19, PICS, prebs, QuasR, Rariant, Repitools, rnaSeqMap, roar, rSFFreader, rtracklayer, segmentSeq, SeqArray, SeqVarTools, ShortRead, 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, SomatiCA, SomaticCancerAlterations, SomaticSignatures, spliceR, SplicingGraphs, TFBSTools, triplex, VanillaICE, VariantFiltering, waveTiling
Suggests Me BeadArrayUseCases, BiocGenerics, interactiveDisplay, IRanges, metaseqR, methylumi, MiRaGE, NarrowPeaks, QDNAseq, SeqGSEA

Package Downloads

Package Source GenomicRanges_1.16.2.tar.gz
Windows Binary GenomicRanges_1.16.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicRanges_1.16.2.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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