This package is for version 3.15 of Bioconductor;
for the stable, up-to-date release version, see
GenomicRanges.
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, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version |
1.48.0 |
| In Bioconductor since |
BioC 2.6 (R-2.11) (12.5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 4.0.0), methods, stats4, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.15.2) |
| Imports |
utils, stats, XVector(>= 0.29.2) |
| LinkingTo |
S4Vectors, IRanges |
| Suggests |
Matrix, Biobase, AnnotationDbi, annotate, Biostrings(>= 2.25.3), SummarizedExperiment(>= 0.1.5), Rsamtools(>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle |
| SystemRequirements |
|
| Enhances |
|
| URL |
https://bioconductor.org/packages/GenomicRanges |
| BugReports |
https://github.com/Bioconductor/GenomicRanges/issues |
| Depends On Me |
AllelicImbalance, AneuFinder, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, baySeq, BindingSiteFinder, biomvRCNS, BiSeq, bnbc, BPRMeth, breakpointR, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, ChAMPdata, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chromPlot, chromstaR, chromswitch, CINdex, cn.mops, cnvGSA, CNVPanelizer, CNVRanger, COCOA, Cogito, compEpiTools, consensusSeekeR, CSAR, csaw, CSSQ, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCFB, DMCHMM, DMRcaller, DMRforPairs, DNAshapeR, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, epihet, esATAC, EuPathDB, ExCluster, exomeCopy, extraChIPs, fastseg, fCCAC, FindIT2, FunChIP, GeneBreak, geneRxCluster, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicFiles, GenomicOZone, GenomicScores, GenomicTuples, gmapR, gmoviz, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, hiAnnotator, HiTC, IdeoViz, igvR, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, liftOver, m6Aboost, maser, MBASED, Melissa, metagene, metagene2, methimpute, methylKit, methylPipe, minfi, MotifDb, msgbsR, MutationalPatterns, NADfinder, nullrangesData, OmicCircos, ORFik, periodicDNA, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, ramr, Rcade, recoup, regioneR, RepViz, rGREAT, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RNAmodR, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, Scale4C, SCATEData, SCOPE, segmentSeq, seqbias, seqCAT, SeqGate, sequencing, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomaticSignatures, spiky, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, TarSeqQC, TnT, trackViewer, TransView, traseR, tRNA, tRNAdbImport, tRNAscanImport, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantTools, VplotR, vtpnet, vulcan, wavClusteR, WGSmapp, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, YAPSA |
| Imports Me |
ACE, ALDEx2, alpine, amplican, AnnotationFilter, annotatr, APAlyzer, apeglm, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, AssessORF, ATACseqQC, atena, BadRegionFinder, ballgown, bambu, bamsignals, BBCAnalyzer, beadarray, BEAT, BiFET, BiocOncoTK, BioPlex, BioTIP, biovizBase, biscuiteer, BiSeq, BOBaFIT, borealis, brainflowprobes, branchpointer, BRGenomics, BSgenome, BUSpaRse, cageminer, CAGEr, cBioPortalData, CexoR, ChAMP, ChIC, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, chromDraw, ChromHeatMap, ChromSCape, chromVAR, cicero, circRNAprofiler, cleanUpdTSeq, cliProfiler, CNEr, CNVfilteR, CNViz, CNVMetrics, comapr, coMET, coMethDMR, compartmap, contiBAIT, conumee, copynumber, CopyNumberPlots, CopywriteR, COSMIC.67, CoverageView, crisprBase, crisprBowtie, CRISPRseek, crisprseekplus, CrispRVariants, customProDB, DAMEfinder, dasper, debrowser, decompTumor2Sig, deconvR, DeepBlueR, DEFormats, DegNorm, deltaCaptureC, derfinder, derfinderPlot, DEWSeq, diffloop, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, DRIMSeq, DropletUtils, easyRNASeq, EDASeq, eisaR, ELMER, ELMER.data, enhancerHomologSearch, enrichTF, epialleleR, EpiCompare, epidecodeR, epigraHMM, epimutacions, epistack, EpiTxDb, epivizr, epivizrData, erma, EventPointer, exomePeak2, fcScan, FilterFFPE, fishpond, fitCons.UCSC.hg19, FLAMES, FRASER, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicDistributionsData, GenomicInteractionNodes, GenomicInteractions, genotypeeval, GenVisR, ggbio, GOfuncR, gpart, GRaNIE, gwascat, h5vc, heatmaps, hermes, HiCBricks, HiCcompare, HiCDCPlus, HilbertCurve, HiLDA, hiReadsProcessor, HTSeqGenie, hummingbird, icetea, ideal, idr2d, IMAS, InPAS, INSPEcT, InterMineR, ipdDb, IsoformSwitchAnalyzeR, isomiRs, iteremoval, IVAS, karyoploteR, leeBamViews, loci2path, LOLA, LoomExperiment, lumi, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, mCSEA, MDTS, MEAL, MEDIPS, megadepth, memes, metaseqR2, MethCP, methInheritSim, MethReg, methrix, methylCC, methylInheritance, MethylSeekR, MethylSeqData, methylSig, methylumi, MinimumDistance, MIRA, missMethyl, mitoClone2, MMAPPR2, MMDiff2, Modstrings, monaLisa, mosaics, Motif2Site, motifbreakR, motifmatchr, MouseFM, MSA2dist, MultiAssayExperiment, multicrispr, MultiDataSet, multiHiCcompare, MungeSumstats, musicatk, NanoMethViz, nanotatoR, ncRNAtools, nearBynding, netDx, NoRCE, normr, nucleR, nullranges, NxtIRFcore, ODER, OGRE, oligoClasses, OmaDB, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, packFinder, pageRank, panelcn.mops, PAST, pcaExplorer, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PhIPData, Pi, PICS, PING, pqsfinder, pram, prebs, preciseTAD, PrecisionTrialDrawer, primirTSS, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, Pviz, pwOmics, QDNAseq, qpgraph, qsea, Qtlizer, R3CPET, R453Plus1Toolbox, RareVariantVis, RCAS, rCGH, RcisTarget, recount, recount3, recountWorkflow, regioneR, regionReport, regutools, REMP, Repitools, rfPred, rGADEM, RGMQL, Rhisat2, RiboCrypt, RiboDiPA, RiboProfiling, RIPAT, RLSeq, Rmmquant, rmspc, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, RTCGAToolbox, scanMiR, scanMiRApp, SCATE, scDblFinder, scmeth, scoreInvHap, scPipe, scRNAseq, scruff, scuttle, segmenter, seq2pathway, SeqArray, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, sevenC, shinyepico, ShortRead, signeR, SigsPack, SimFFPE, SingleCellExperiment, SingleMoleculeFootprinting, sitadela, snapcount, 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, SNPlocs.Hsapiens.dbSNP151.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticCancerAlterations, SparseSignatures, spatialLIBD, spatzie, SpectralTAD, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, systemPipeR, TAPseq, target, TCGAbiolinks, TCGAutils, TCGAWorkflow, TCseq, terraTCGAdata, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, tidybulk, TitanCNA, tLOH, tracktables, transcriptR, transite, trena, TRESS, tricycle, triplex, tscR, TSRchitect, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, uncoverappLib, Uniquorn, VariantFiltering, VariantToolsData, VaSP, VCFArray, wiggleplotr, xcore, XNAString, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 |
| Suggests Me |
alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, AnnotationHub, autonomics, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, CAGEWorkflow, Chicago, CNVgears, ComplexHeatmap, cummeRbund, epivizrChart, GenomeInfoDb, GenomicState, GeuvadisTranscriptExpr, ggmanh, Glimma, GSReg, GWASTools, HDF5Array, InteractiveComplexHeatmap, interactiveDisplay, IRanges, maftools, MiRaGE, nanotubes, omicsPrint, Onassis, parglms, plotgardener, recountmethylation, RNAmodR.Data, RTCGA, S4Vectors, SeqGSEA, Single.mTEC.Transcriptomes, splatter, systemPipeRdata, TFutils, universalmotif, updateObject, xcoredata |
| Links To Me |
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| Build Report |
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