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 |
1.30.3 |
| In Bioconductor since |
BioC 2.6 (R-2.11) (8 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.10), methods, stats4, BiocGenerics(>= 0.21.2), S4Vectors(>= 0.9.47), IRanges(>= 2.11.16), GenomeInfoDb(>= 1.13.1) |
| 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), Matrix, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, 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, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, RNAseqData.HNRNPC.bam.chr14, hgu95av2probe |
| SystemRequirements |
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| Enhances |
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| URL |
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| Depends On Me |
AllelicImbalance, AneuFinder, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, baySeq, biomvRCNS, BiSeq, bnbc, BPRMeth, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, casper, ChAMPdata, cheung2010, chimera, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chroGPS, chromPlot, chromstaR, chromswitch, CINdex, cleanUpdTSeq, cn.mops, CNPBayes, cnvGSA, CNVPanelizer, compEpiTools, consensusSeekeR, CSAR, csaw, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DMCHMM, DMRcaller, DMRcatedata, DMRforPairs, DNAshapeR, DOQTL, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, esATAC, exomeCopy, fastseg, fCCAC, FourCSeq, FunChIP, GeneBreak, geneRxCluster, GenoGAM, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicScores, GenomicTuples, genoset, geuvStore2, gmapR, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, hiAnnotator, HilbertCurve, HiTC, htSeqTools, IdeoViz, InPAS, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, MBASED, metagene, methimpute, methyAnalysis, methylKit, methylPipe, minfi, msgbsR, MutationalPatterns, NADfinder, OmicCircos, PGA, PING, podkat, QuasR, r3Cseq, RaggedExperiment, Rariant, Rcade, recoup, regioneR, rfPred, rGREAT, riboSeqR, RIPSeeker, RJMCMCNucleosomes, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, Scale4C, segmentSeq, seqbias, seqCAT, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomaticSignatures, SummarizedExperiment, TarSeqQC, TnT, trackViewer, TransView, traseR, VanillaICE, VariantAnnotation, VariantTools, vtpnet, vulcan, wavClusteR, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, YAPSA |
| Imports Me |
ALDEx2, alpine, amplican, AnnotationFilter, annotatr, apeglm, ArrayExpressHTS, ASpli, ATACseqQC, BadRegionFinder, ballgown, bamsignals, BBCAnalyzer, beadarray, BEAT, biovizBase, BiSeq, branchpointer, BSgenome, CAGEr, CexoR, cgdv17, ChAMP, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, chromDraw, ChromHeatMap, chromVAR, CNEr, coMET, contiBAIT, conumee, copynumber, CopywriteR, COSMIC.67, CoverageView, crisprseekplus, CrispRVariants, customProDB, DChIPRep, debrowser, DeepBlueR, DEFormats, derfinder, derfinderPlot, diffloop, DMRcate, DMRScan, DRIMSeq, easyRNASeq, EDASeq, ELMER, ELMER.data, epivizr, epivizrData, erma, EventPointer, fitCons.UCSC.hg19, flipflop, FourCSeq, FunciSNP, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicInteractions, genotypeeval, GenVisR, GGBase, ggbio, GGtools, GoogleGenomics, gQTLBase, gQTLstats, gwascat, h5vc, heatmaps, HiCcompare, hiReadsProcessor, HTSeqGenie, ideal, IMAS, INSPEcT, InterMineR, IsoformSwitchAnalyzeR, isomiRs, IVAS, JunctionSeq, karyoploteR, leeBamViews, LOLA, lumi, M3D, MADSEQ, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.TOPMed.freeze5.hg38, MEAL, MEDIPS, methInheritSim, methyAnalysis, methylInheritance, MethylSeekR, methylumi, MinimumDistance, MIRA, MMDiff2, mosaics, motifbreakR, motifmatchr, MultiAssayExperiment, MultiDataSet, NarrowPeaks, normr, nucleR, oligoClasses, openPrimeR, Organism.dplyr, OrganismDbi, panelcn.mops, Pbase, pcaExplorer, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, PICS, pqsfinder, prebs, proBAMr, PureCN, Pviz, pwOmics, QDNAseq, qpgraph, qsea, R3CPET, R453Plus1Toolbox, RareVariantVis, RCAS, rCGH, recount, regioneR, regionReport, REMP, Repitools, RiboProfiling, RNAprobR, rnaSeqMap, roar, RTCGAToolbox, scoreInvHap, seq2pathway, SeqArray, seqPattern, seqplots, SeqSQC, SeqVarTools, ShortRead, signeR, simulatorZ, SNPchip, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, soGGi, SomaticCancerAlterations, spliceR, SplicingGraphs, SPLINTER, STAN, SVM2CRM, systemPipeR, TCGAbiolinks, TCseq, TFARM, TFBSTools, TFHAZ, TitanCNA, tracktables, transcriptR, TReNA, trena, triplex, TSRchitect, TVTB, VariantFiltering, VariantToolsData, waveTiling, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, yriMulti |
| Suggests Me |
alternativeSplicingEvents.hg19, AnnotationHub, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, Chicago, cummeRbund, epivizrChart, GenomeInfoDb, GeuvadisTranscriptExpr, GSReg, GWASTools, HDF5Array, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, NGScopy, Onassis, RTCGA, S4Vectors, SeqGSEA, Single.mTEC.Transcriptomes |
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