IRanges
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This package is for version 2.12 of Bioconductor;
for the stable, up-to-date release version, see
IRanges.
Infrastructure for manipulating intervals on sequences
Bioconductor version: 2.12
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
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R,
enter citation("IRanges")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IRanges")
Documentation
To view documentation for the version of this package installed
in your system, start R and enter:
browseVignettes("IRanges")
Details
| biocViews |
DataRepresentation, Infrastructure, Software |
| Version |
1.18.4 |
| In Bioconductor since |
BioC 2.3 (R-2.8) (7.5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.8.0), methods, utils, stats, BiocGenerics(>= 0.5.6) |
| Imports |
methods, utils, stats, BiocGenerics, stats4 |
| LinkingTo |
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| Suggests |
GenomicRanges, RUnit, BSgenome.Celegans.UCSC.ce2 |
| 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, casper, ChIPpeakAnno, chipseq, chroGPS, cn.mops, CSAR, DASiR, DECIPHER, deepSNV, DESeq2, DirichletMultinomial, easyRNASeq, epigenomix, exomeCopy, genomes, GenomicFeatures, GenomicRanges, Genominator, genoset, GGtools, girafe, gwascat, harbChIP, HiTC, HMMcopy, htSeqTools, LiebermanAidenHiC2009, methyAnalysis, MinimumDistance, MotifDb, nucleR, oneChannelGUI, PING, rGADEM, RIPSeeker, rMAT, Rsamtools, rSFFreader, segmentSeq, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SplicingGraphs, TEQC, triform, VariantAnnotation, VariantTools, xmapcore |
| Imports Me |
annmap, AnnotationDbi, ArrayExpressHTS, BayesPeak, Biostrings, biovizBase, BiSeq, BitSeq, CAGEr, cgdv17, charm, ChIPpeakAnno, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cn.mops, copynumber, DECIPHER, DESeq2, DiffBind, EDASeq, ensemblVEP, epigenomix, fastseg, flowQ, FunciSNP, gCMAPWeb, gcrma, GenomicFeatures, GenomicRanges, ggbio, girafe, gmapR, Gviz, HTSeqGenie, HTSFilter, MEDIPS, methVisual, methyAnalysis, MethylSeekR, MMDiff, mosaics, motifRG, MotIV, MSnbase, NarrowPeaks, nucleR, oligoClasses, OTUbase, 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.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.atdschip.tiling, 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.charm.hg18.example, pd.chicken, 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.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, 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.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.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.3.1, 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.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.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.1.1.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.1.1.st, pd.rn.u34, pd.s.aureus, pd.soybean, 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, pdInfoBuilder, PICS, prebs, QuasR, R453Plus1Toolbox, Rcade, REDseq, Repitools, rGADEM, rMAT, rnaSeqMap, Rolexa, Rsamtools, rSFFreader, RSVSim, rtracklayer, segmentSeq, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SplicingGraphs, TransView, triform, TSSi, VanillaICE, VariantAnnotation, VariantTools, waveTiling |
| Suggests Me |
BiocGenerics, HilbertVis, HilbertVisGUI, MiRaGE, Repitools, SNPchip, yeastRNASeq |
| Build Report |
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