IRanges

Infrastructure for manipulating intervals on sequences

Bioconductor version: 2.8

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: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("IRanges")

To cite this package in a publication, start R and enter:

    citation("IRanges")

Documentation

PDF R Script An Introduction to IRanges
PDF R Script Rle Tips and Tricks
PDF   Reference Manual

Details

biocViews Infrastructure, DataRepresentation
Depends R (>= 2.8.0), methods, utils, stats
Imports methods, utils, stats
Suggests RUnit
System Requirements
License Artistic-2.0
URL
Depends On Me BayesPeak, Biostrings, BSgenome, ChIPpeakAnno, chipseq, GenomicFeatures, GenomicRanges, Genominator, genoset, GGtools, girafe, harbChIP, oneChannelGUI, PICS, rGADEM, rMAT, Rsamtools, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, TEQC, VanillaICE, xmapcore
Imports Me ArrayExpressHTS, BayesPeak, Biostrings, charm, ChIPpeakAnno, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, GenomicFeatures, GenomicRanges, genoset, GGtools, girafe, MEDIPS, methVisual, mosaics, MotIV, MSnbase, 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.barley1, pd.bovine, pd.bsubtilis, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, 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.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.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.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.rat230.2, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhesus, pd.rice, pd.rn.u34, pd.s.aureus, pd.soybean, 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.zebrafish, pdInfoBuilder, PICS, R453Plus1Toolbox, rGADEM, rMAT, rnaSeqMap, Rolexa, Rsamtools, rtracklayer, segmentSeq, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, TEQC
Suggests Me HilbertVis, HilbertVisGUI, oneChannelGUI, yeastRNASeq
Version 1.10.6
Since Bioconductor 2.3 (R-2.8)

Package Downloads

Package Source IRanges_1.10.6.tar.gz
Windows Binary IRanges_1.10.6.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary IRanges_1.10.6.tgz
Package Downloads Report Download Stats

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