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Bioconductor - IRanges (development version)

IRanges

This is the development version of IRanges; for the stable release version, see IRanges.

Foundation of integer range manipulation in Bioconductor

Bioconductor version: Development (3.22)

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.

Author: Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("IRanges")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("IRanges")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IRanges")
Details See More Suggests XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle Linking To S4Vectors Enhances Depends On Me AnnotationDbi, AnnotationHubData, BaalChIP, bambu, biomvRCNS, Biostrings, BiSeq, BSgenome, BSgenomeForge, BubbleTree, bumphunter, CAFE, casper, CexoR, chimeraviz, ChIPpeakAnno, chipseq, CODEX, consensusSeekeR, CSAR, CSSQ, customProDB, deepSNV, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCFB, DMCHMM, DMRcaller, epigenomix, ExCluster, fCCAC, GenomeInfoDb, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicRanges, groHMM, gtrellis, Gviz, HelloRanges, HERON, HiTC, IdeoViz, InTAD, MotifDb, MultimodalExperiment, NADfinder, oncoscanR, ORFik, OTUbase, pepStat, periodicDNA, plyranges, proBAMr, pwalign, RepViz, rGREAT, RJMCMCNucleosomes, RNAmodR, S4Arrays, Scale4C, SCOPE, seqArchRplus, SGSeq, SICtools, Structstrings, TEQC, traseR, triplex, VariantTools, VplotR, XVector, 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, harbChIP, LiebermanAidenHiC2009 Imports Me alabaster.bumpy, alabaster.ranges, alabaster.se, ALDEx2, AllelicImbalance, amplican, annmap, annotatr, appreci8R, ASpli, AssessORF, ATACseqQC, ATACseqTFEA, atena, ballgown, bamsignals, BBCAnalyzer, beadarray, BindingSiteFinder, biovizBase, biscuiteer, BiSeq, bnbc, BPRMeth, branchpointer, breakpointR, bsseq, BUMHMM, BumpyMatrix, BUSpaRse, CAGEfightR, cageminer, CAGEr, cBioPortalData, cfdnakit, cfDNAPro, ChIPanalyser, chipenrich, ChIPexoQual, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, chromVAR, cicero, CINdex, circRNAprofiler, CircSeqAlignTk, cleanUpdTSeq, cleaver, cn.mops, CNVfilteR, CNVMetrics, CNVPanelizer, CNVRanger, CNVrd2, COCOA, comapr, coMethDMR, ComplexHeatmap, CompoundDb, conumee, CopyNumberPlots, CoverageView, crisprBase, crisprBowtie, crisprDesign, crisprScore, CRISPRseek, CrispRVariants, crisprViz, crupR, csaw, CTexploreR, dada2, DAMEfinder, debrowser, DECIPHER, deconvR, DegCre, DegNorm, DelayedMatrixStats, deltaCaptureC, demuxSNP, derfinder, derfinderHelper, derfinderPlot, DEScan2, DiffBind, diffHic, diffUTR, DMRcate, DMRScan, dmrseq, DNAfusion, DominoEffect, dreamlet, DRIMSeq, DropletUtils, dStruct, easyRNASeq, EDASeq, eisaR, ELMER, ELViS, enhancerHomologSearch, EnrichedHeatmap, ensembldb, EpiCompare, epidecodeR, epigraHMM, EpiMix, epimutacions, epiregulon, epistack, EpiTxDb, epivizr, epivizrData, esATAC, EventPointer, extraChIPs, factR, FastqCleaner, fastseg, fcScan, FilterFFPE, FindIT2, fishpond, FLAMES, FRASER, G4SNVHunter, GA4GHclient, gcapc, gDNAx, geneAttribution, GENESIS, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicPlot, GenomicScores, GenomicTuples, GenVisR, geomeTriD, ggbio, gmapR, gmoviz, GOfuncR, GOpro, GOTHiC, GSVA, GUIDEseq, gwascat, h5mread, h5vc, HDF5Array, heatmaps, hermes, HicAggR, HiCBricks, HiCcompare, HiCExperiment, HiContacts, HiCool, hicVennDiagram, HilbertCurve, hummingbird, icetea, ideal, idr2d, igblastr, IMAS, InPAS, INSPEcT, intansv, InteractionSet, InteractiveComplexHeatmap, IntEREst, ipdDb, iSEEu, IsoformSwitchAnalyzeR, isomiRs, IVAS, karyoploteR, katdetectr, knowYourCG, LinTInd, LOLA, m6Aboost, magpie, mariner, maser, MatrixRider, mCSEA, MDTS, MEAL, MEDIPS, MesKit, metagene2, metaseqR2, methimpute, methInheritSim, methodical, MethReg, methrix, methylCC, methylInheritance, methylKit, methylPipe, MethylSeekR, methylSig, methylumi, mia, minfi, MinimumDistance, MIRA, missMethyl, 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, NanoMethViz, NanoStringNCTools, ncRNAtools, normr, nucleoSim, nucleR, nullranges, OGRE, oligoClasses, OmaDB, OMICsPCA, Organism.dplyr, OrganismDbi, OUTRIDER, OutSplice, packFinder, panelcn.mops, pcaExplorer, pdInfoBuilder, PhIPData, PICB, plotgardener, plyinteractions, podkat, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, profileplyr, ProteoDisco, PSMatch, PureCN, Pviz, QDNAseq, QFeatures, qpgraph, qPLEXanalyzer, qsea, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, raer, RaggedExperiment, RAIDS, ramr, RareVariantVis, RCAS, recount, recoup, REDseq, regioneR, regutools, REMP, Repitools, ReportingTools, RESOLVE, rfaRm, rfPred, RgnTX, RiboCrypt, RiboDiPA, RiboProfiling, riboSeqR, ribosomeProfilingQC, rigvf, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, roar, rprimer, Rqc, Rsamtools, RSVSim, RTN, rtracklayer, SARC, sarks, saseR, SCAN.UPC, scanMiR, scanMiRApp, scDblFinder, scHOT, scPipe, scRNAseqApp, segmenter, segmentSeq, SeqArray, seqCAT, Seqinfo, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sevenC, ShortRead, signeR, signifinder, SimFFPE, SingleMoleculeFootprinting, sitadela, Site2Target, SMITE, snapcount, SNPhood, soGGi, SomaticSignatures, SOMNiBUS, SparseArray, SparseSignatures, spatzie, Spectra, spiky, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, StructuralVariantAnnotation, SummarizedExperiment, SynExtend, tadar, TAPseq, target, TCGAbiolinks, TCGAutils, TCseq, TENET, TFBSTools, TFEA.ChIP, TFHAZ, tidyCoverage, TnT, tracktables, trackViewer, transcriptR, transmogR, TreeSummarizedExperiment, TRESS, tricycle, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, txdbmaker, tximeta, UMI4Cats, Uniquorn, universalmotif, UPDhmm, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantFiltering, VaSP, VDJdive, vmrseq, wavClusteR, wiggleplotr, xcms, xcore, XVector, yamss, ZygosityPredictor, fitCons.UCSC.hg19, GenomicState, 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, 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.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, chipenrich.data, fourDNData, leeBamViews, MethylSeqData, pd.atdschip.tiling, sesameData, SomaticCancerAlterations, spatialLIBD, seqpac, alakazam, cpp11bigwig, crispRdesignR, cubar, geneHapR, geno2proteo, GenoPop, hahmmr, HiCociety, hoardeR, ICAMS, iimi, karyotapR, locuszoomr, lolliplot, longreadvqs, LoopRig, MAAPER, MitoHEAR, noisyr, numbat, oncoPredict, PACVr, RapidoPGS, refseqR, revert, rnaCrosslinkOO, RTIGER, SATS, Signac, tidygenomics, VALERIE Suggests Me annotate, AnnotationHub, BaseSpaceR, BiocGenerics, BREW3R.r, CCAFE, Chicago, ClassifyR, DFplyr, easylift, epivizrChart, gDRcore, gDRutils, Glimma, GWASTools, HilbertVis, HilbertVisGUI, maftools, martini, MiRaGE, multicrispr, partCNV, plyxp, regionalpcs, regionReport, RTCGA, S4Vectors, SigsPack, splatter, svaNUMT, svaRetro, systemPipeR, TFutils, tidybulk, MetaScope, scMultiome, systemPipeRdata, xcoredata, yeastRNASeq, fuzzyjoin, GencoDymo2, gkmSVM, MARVEL, MiscMetabar, polyRAD, pQTLdata, rliger, scPloidy, seqmagick, Seurat, sigminer, SNPassoc, updog, valr Links To Me Biostrings, DECIPHER, GenomicAlignments, GenomicRanges, kebabs, MatrixRider, pwalign, Rsamtools, rtracklayer, ShortRead, SparseArray, Structstrings, triplex, VariantAnnotation, VariantFiltering, XVector Build Report Build Report Package Archives

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