To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IRanges")

In most cases, you don't need to download the package archive at all.

IRanges

   

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see 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>

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")

 

PDF IRangesOverview.pdf
PDF RleTricks.pdf
PDF   Reference Manual

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.10.6
In Bioconductor since BioC 2.3 (R-2.8) (7.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, utils, stats
Imports methods, utils, stats
LinkingTo
Suggests RUnit
SystemRequirements
Enhances
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
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source IRanges_1.10.6.tar.gz
Windows Binary IRanges_1.10.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/IRanges/tree/release-2.8
Package Short Url http://bioconductor.org/packages/IRanges/
Package Downloads Report Download Stats

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