The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.
Author: H. Pages, P. Aboyoun and M. Lawrence
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| biocViews |
DataRepresentation, Infrastructure, Software |
| Version |
2.0.1 |
| In Bioconductor since |
BioC 2.3 (R-2.8) |
| License |
Artistic-2.0 |
| Depends |
R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.2.5) |
| Imports |
stats4 |
| LinkingTo |
S4Vectors |
| Suggests |
XVector, GenomicRanges, BSgenome.Celegans.UCSC.ce2, RUnit |
| SystemRequirements |
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| Enhances |
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| URL |
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| Depends On Me |
AnnotationHub, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, bsseq, bumphunter, CAFE, casper, CexoR, ChIPpeakAnno, chipseq, chroGPS, cn.mops, CSAR, customProDB, DASiR, deepSNV, DESeq2, DEXSeq, DirichletMultinomial, DNaseR, epigenomix, exomeCopy, geneRxCluster, GenomeInfoDb, genomes, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, girafe, groHMM, Gviz, harbChIP, HiTC, HMMcopy, htSeqTools, IdeoViz, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, nucleR, oneChannelGUI, 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.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.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.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, 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.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, PING, proBAMr, PSICQUIC, RefNet, rfPred, rGADEM, RIPSeeker, rMAT, Rsamtools, scsR, segmentSeq, SGSeq, 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, SomatiCA, SplicingGraphs, TEQC, TitanCNA, triform, triplex, TSSi, VariantTools, XVector |
| Imports Me |
AllelicImbalance, annmap, ArrayExpressHTS, ballgown, BayesPeak, beadarray, Biostrings, biovizBase, BiSeq, BitSeq, BSgenome, CAGEr, cgdv17, charm, chipenrich, chipenrich.data, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cleaver, CNEr, CNVrd2, cobindR, compEpiTools, copynumber, CoverageView, csaw, customProDB, DECIPHER, derfinder, derfinderHelper, derfinderPlot, DiffBind, DOQTL, easyRNASeq, EDASeq, facopy, fastseg, flipflop, flowQ, FunciSNP, gCMAPWeb, GenomicAlignments, GenomicFiles, GenomicInteractions, genoset, ggbio, GGtools, girafe, gmapR, GOTHiC, gwascat, h5vc, HTSeqGenie, HTSFilter, intansv, M3D, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MEDIPS, methVisual, methyAnalysis, methylPipe, MethylSeekR, methylumi, minfi, MinimumDistance, MMDiff, mosaics, motifRG, MotIV, MSnbase, NarrowPeaks, nucleR, oligoClasses, Pbase, 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.hg18.60mer.expr, pd.mirna.3.1, pd.mogene.2.0.st, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pdInfoBuilder, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg19, PICS, plethy, polyester, prebs, Pviz, qpgraph, QuasR, R453Plus1Toolbox, Rariant, REDseq, regionReport, Repitools, ReportingTools, rGADEM, rMAT, rnaSeqMap, Rolexa, Rqc, rSFFreader, RSVSim, RTN, rtracklayer, SCAN.UPC, SeqArray, seqplots, SeqVarTools, ShortRead, 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, SomatiCA, SomaticCancerAlterations, SomaticSignatures, spliceR, SplicingGraphs, TFBSTools, tracktables, TransView, triform, TSSi, VanillaICE, VariantAnnotation, VariantFiltering, wavClusteR, waveTiling, XVector |
| Suggests Me |
BaseSpaceR, BiocGenerics, HilbertVis, HilbertVisGUI, MiRaGE, S4Vectors, STAN, yeastRNASeq |
| Build Report |
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