The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure.
Author: P. Aboyoun, H. Pagès, and M. Lawrence
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| biocViews |
Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version |
1.22.4 |
| In Bioconductor since |
BioC 2.6 (R-2.11) (6 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.10), methods, BiocGenerics(>= 0.16.1), S4Vectors(>= 0.8.6), IRanges(>= 2.4.6), GenomeInfoDb(>= 1.1.20) |
| Imports |
utils, stats, XVector |
| LinkingTo |
S4Vectors, IRanges |
| Suggests |
Biobase, AnnotationDbi(>= 1.21.1), annotate, Biostrings(>= 2.25.3), Rsamtools(>= 1.13.53), SummarizedExperiment(>= 0.1.5), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements |
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| Enhances |
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| URL |
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| Depends On Me |
AllelicImbalance, annmap, AnnotationHubData, Basic4Cseq, baySeq, biomvRCNS, BiSeq, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, casper, cheung2010, chimera, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, cleanUpdTSeq, cn.mops, CNPBayes, cnvGSA, CNVPanelizer, compEpiTools, CSAR, csaw, DASiR, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DMRcaller, DMRcatedata, DMRforPairs, DOQTL, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, exomeCopy, fastseg, FourCSeq, GeneBreak, geneRxCluster, genomes, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicTuples, genoset, GenoView, geuvStore, ggtut, gmapR, GOTHiC, GreyListChIP, groHMM, Guitar, Gviz, hiAnnotator, HilbertCurve, HiTC, htSeqTools, IdeoViz, InPAS, intansv, MBASED, metagene, methyAnalysis, methylPipe, minfi, MMDiff, OmicCircos, PGA, PING, podkat, QuasR, r3Cseq, Rariant, Rcade, regioneR, rfPred, rGREAT, riboSeqR, RIPSeeker, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, segmentSeq, seqbias, SGSeq, SigFuge, SNPhood, 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, SummarizedExperiment, TarSeqQC, trackViewer, TransView, traseR, VanillaICE, VariantAnnotation, VariantTools, vtpnet, wavClusteR, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38 |
| Imports Me |
ALDEx2, ArrayExpressHTS, ballgown, bamsignals, beadarray, BEAT, biovizBase, BiSeq, BSgenome, CAGEr, CexoR, cgdv17, ChAMP, chipenrich, chipenrich.data, ChIPseeker, chipseq, ChIPseqR, chromDraw, CNEr, coMET, conumee, copynumber, CopywriteR, COSMIC.67, CoverageView, customProDB, DChIPRep, derfinder, derfinderPlot, DMRcate, easyRNASeq, EDASeq, ELMER, ELMER.data, epivizr, erma, flipflop, FourCSeq, FunciSNP, genomation, genomeIntervals, GenomicAlignments, GenomicInteractions, genotypeeval, GGBase, ggbio, GGtools, GoogleGenomics, gQTLBase, gQTLstats, GUIDEseq, gwascat, h5vc, hiReadsProcessor, HTSeqGenie, INSPEcT, IVAS, LedPred, leeBamViews, LOLA, lumi, M3D, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ALL.wgs.phase3.release.v5b.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, MEAL, MEDIPS, methyAnalysis, MethylSeekR, methylumi, MinimumDistance, MMDiff, motifbreakR, NarrowPeaks, nucleR, oligoClasses, OrganismDbi, Pbase, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PICS, prebs, proBAMr, Pviz, pwOmics, qpgraph, R3CPET, R453Plus1Toolbox, RareVariantVis, rCGH, regioneR, regionReport, Repitools, rgsepd, RiboProfiling, RNAprobR, rnaSeqMap, roar, seq2pathway, SeqArray, seqPattern, seqplots, SeqVarTools, ShortRead, SICtools, 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, TCGAbiolinks, TFBSTools, ToPASeq, tracktables, triplex, VariantFiltering, waveTiling, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 |
| Suggests Me |
AnnotationHub, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, cummeRbund, GenomeInfoDb, gtrellis, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, NGScopy, SeqGSEA, STAN |
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