IRanges
Foundation of integer range manipulation in Bioconductor
Bioconductor version: 3.23 · Package version: 2.46.0
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IRanges")Details
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| Author | Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/IRanges |
| Bug Reports | https://github.com/Bioconductor/IRanges/issues |
| Downloads rank | 65232 |
| Source branch | RELEASE_3_23 |
| biocViews | DataRepresentation, Infrastructure, Software |
Documentation
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Dependencies
Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6)
Imports: stats4
LinkingTo: S4Vectors
Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle
Reverse dependencies
Depends On Me (240): AnnotationDbi, AnnotationHubData, BaalChIP, bambu, biomvRCNS, Biostrings, BiSeq, BSgenome, BSgenomeForge, BubbleTree, bumphunter, CAFE, casper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, cigarillo, CODEX, consensusSeekeR, CSAR, CSSQ, customProDB, deepSNV, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCFB, DMCHMM, DMRcaller, epigenomix, ExCluster, fCCAC, geneRxCluster, GenomeInfoDb, GenomicAlignments, GenomicCoordinates, GenomicDistributions, GenomicFeatures, GenomicRanges, groHMM, gtrellis, Gviz, harbChIP, HelloRanges, HERON, HiTC, IdeoViz, InTAD, LiebermanAidenHiC2009, MotifDb, MultimodalExperiment, NADfinder, oncoscanR, ORFik, OTUbase, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, pd.citrus, pd.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hta.2.0, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.4.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rabgene.1.0.st, pd.rabgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.0.st, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, pepStat, periodicDNA, plyranges, proBAMr, pwalign, RepViz, rGREAT, RJMCMCNucleosomes, RNAmodR, S4Arrays, Scale4C, SCOPE, SGSeq, SICtools, Structstrings, TEQC, traseR, triplex, VariantTools, VplotR, XVector
Imports Me (536): AbSolution, ActiveDriverWGS, alabaster.bumpy, alabaster.ranges, alabaster.se, alakazam, ALDEx2, AllelicImbalance, amplican, annmap, annoLinker, annotatr, appreci8R, ASpli, AssessORF, ATACseqQC, ATACseqTFEA, atena, ballgown, bamsignals, BasicSTARRseq, BBCAnalyzer, beadarray, betterChromVAR, BgeeCall, BindingSiteFinder, Bioc.gff, biovizBase, biscuiteer, BiSeq, bnbc, BPRMeth, branchpointer, breakpointR, bsseq, BUMHMM, BumpyMatrix, BUSpaRse, CAGEfightR, cageminer, CAGEr, cBioPortalData, cfdnakit, cfDNAPro, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, ChromSCape, chromVAR, cicero, circRNAprofiler, CircSeqAlignTk, cleanUpdTSeq, cleaver, ClonalSim, cn.mops, CNEr, CNVfilteR, CNVMetrics, CNVPanelizer, CNVRanger, CNVrd2, COCOA, comapr, coMethDMR, compEpiTools, ComplexHeatmap, CompoundDb, conumee, CopyNumberPlots, CoverageView, cpp11bigwig, crisprBase, crisprBowtie, crisprDesign, crispRdesignR, crisprScore, CRISPRseek, CrispRVariants, crisprViz, crupR, csaw, CTexploreR, cubar, dada2, DAMEfinder, damidBind, debrowser, decemedip, DECIPHER, deconvR, DegCre, DegNorm, DelayedMatrixStats, deltaCaptureC, demuxSNP, derfinder, derfinderHelper, derfinderPlot, DEScan2, DESNP, DiffBind, diffHic, diffUTR, DMRcaller, DMRcate, DMRScan, dmrseq, DNAfusion, DominoEffect, DOTSeq, dreamlet, DRIMSeq, DropletUtils, dStruct, easyRNASeq, EDASeq, eisaR, ELMER, ELViS, enhancerHomologSearch, ENmix, EnrichedHeatmap, ensembldb, EpiCompare, epidecodeR, epigraHMM, EpiMix, epimutacions, epiregulon, epiRomics, epiSeeker, epistack, EpiTxDb, epivizr, epivizrData, esATAC, EventPointer, extraChIPs, factR, FastqCleaner, fastRanges, fastseg, fcScan, FilterFFPE, FindIT2, fishpond, fitCons.UCSC.hg19, FLAMES, fourDNData, fRagmentomics, FRASER, G4SNVHunter, GA4GHclient, gcapc, gDNAx, GencoDymo2, geneAttribution, GENESIS, GeneStructureTools, geno2proteo, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicPlot, GenomicScores, GenomicState, GenomicTuples, GenoPop, GenVisR, geomeTriD, ggbio, gmapR, gmoviz, GOfuncR, GOpro, GOTHiC, GSVA, GUIDEseq, gVenn, gwascat, h5mread, h5vc, hahmmr, HDF5Array, heatmaps, hermes, HicAggR, HiCaptuRe, HiCBricks, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, HiCPotts, hicVennDiagram, HilbertCurve, hummingbird, icetea, ideal, idr2d, igblastr, iimi, imageFeatureTCGA, IMAS, InPAS, INSPEcT, intansv, InteractionSet, InteractiveComplexHeatmap, IntEREst, ipdDb, iSEEu, IsoformSwitchAnalyzeR, isomiRs, IVAS, IWTomics, karyoploteR, karyotapR, katdetectr, knowYourCG, leeBamViews, linkSet, lisat, locuszoomr, LOLA, longreadvqs, LoopRig, m6Aboost, 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.v4.0.GRCh38, magpie, mariner, maser, MatrixRider, mCSEA, MDTS, MEAL, MEDIPS, MesKit, metagene2, metaseqR2, methimpute, methInheritSim, methodical, MethReg, methrix, methylCC, methylInheritance, methylKit, methylPipe, MethylSeekR, MethylSeqData, methylSig, methylumi, mia, minfi, MinimumDistance, MIRA, missMethyl, MitoHEAR, mobileRNA, Modstrings, monaLisa, mosaics, MOSim, Motif2Site, motifbreakR, motifmatchr, MotifPeeker, motifTestR, MouseFM, msa, MSA2dist, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsExperiment, msgbsR, MSnbase, MultiAssayExperiment, MultiDataSet, mumosa, MungeSumstats, musicatk, MutationalPatterns, mutscan, MutSeqR, NanoMethViz, NanoStringNCTools, ncRNAtools, noisyr, NoRCE, normr, nucleoSim, nucleR, nullranges, numbat, OGRE, oligoClasses, OmaDB, OMICsPCA, oncoPredict, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, OutSplice, packFinder, PACVr, panelcn.mops, pcaExplorer, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.atdschip.tiling, pd.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, pdInfoBuilder, peakCombiner, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PhIPData, PICB, PlinkMatrix, plotgardener, plyinteractions, podkat, postNet, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, profileplyr, ProteoDisco, PureCN, Pviz, QDNAseq, QFeatures, qpgraph, qPLEXanalyzer, qsea, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, raer, RaggedExperiment, RAIDS, ramr, RapidoPGS, RareVariantVis, RBedMethyl, RCAS, rCGH, recount, recoup, REDseq, refseqR, regioneR, regutools, REMP, ReportingTools, RESOLVE, revert, rfaRm, rfPred, RgnTX, RiboCrypt, RiboDiPA, RiboProfiling, riboSeqR, ribosomeProfilingQC, rigvf, rnaCrosslinkOO, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAshapeQC, RnBeads, roar, rprimer, Rqc, Rsamtools, RSVSim, RTN, rtracklayer, sarks, saseR, SATS, SCAN.UPC, scanMiR, scanMiRApp, SCANVIS, scDblFinder, scHOT, scPipe, scRNAseqApp, segmenter, segmentSeq, SeqArray, seqCAT, Seqinfo, seqpac, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, sevenC, ShortRead, Signac, signeR, signifinder, SimFFPE, sitadela, Site2Target, SMITE, snapcount, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticCancerAlterations, SomaticSignatures, SOMNiBUS, SparseArray, SparseSignatures, spatialLIBD, spatzie, Spectra, SpectriPy, spiky, SpliceImpactR, splicelogic, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, STADyUM, strandCheckR, StructuralVariantAnnotation, SummarizedExperiment, SynExtend, tadar, TAPseq, target, TCGAbiolinks, TCGAutils, TCseq, TENET, TFBSTools, TFEA.ChIP, TFHAZ, tidyCoverage, TmCalculator, TnT, toppgene, tracktables, trackViewer, transcriptR, transmogR, TreeSummarizedExperiment, TRESS, tricycle, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, txdbmaker, tximeta, UMI4Cats, Uniquorn, universalmotif, UPDhmm, VALERIE, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantFiltering, VaSP, VDJdive, vmrseq, wavClusteR, wiggleplotr, xcms, xcore, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss, ZarrArray, ZygosityPredictor
Suggests Me (63): annotate, AnnotationHub, BaseSpaceR, BiocGenerics, BREW3R.r, CCAFE, Chicago, Chromatograms, ClassifyR, CNVScope, DFplyr, easylift, epivizrChart, fuzzyjoin, gDRcore, gDRutils, gggenomes, gkmSVM, Glimma, GWASTools, HilbertVis, HilbertVisGUI, Immutables, iscream, LACHESIS, lncRna, maftools, martini, MetaScope, MiRaGE, MiscMetabar, MoBPS, multicrispr, partCNV, plyxp, polyRAD, pQTLdata, regionalpcs, regionReport, rliger, RTCGA, S4Vectors, scMultiome, scPloidy, scrapper, SEMPLR, seqmagick, Seurat, sigminer, SigsPack, SNPassoc, splatter, svaNUMT, svaRetro, systemPipeR, systemPipeRdata, TFutils, tidybulk, updog, valr, vectra, xcoredata, yeastRNASeq
Links To Me (21): Bioc.gff, Biostrings, cigarillo, CNEr, DECIPHER, DegNorm, GenomicAlignments, GenomicFeatures, kebabs, MatrixRider, posDemux, pwalign, Rsamtools, rtracklayer, ShortRead, SparseArray, Structstrings, triplex, VariantAnnotation, VariantFiltering, XVector