IRanges

Infrastructure for manipulating intervals on sequences

Bioconductor version: 2.7

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, as well as views on these sequences. 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 "Sequence 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, biocDatasets, Biostrings, BSgenome, ChIPpeakAnno, chipseq, GenomicFeatures, GenomicRanges, Genominator, GGtools, girafe, harbChIP, oneChannelGUI, PICS, rGADEM, rMAT, Rsamtools, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, VanillaICE, xmapcore
Imports Me	BayesPeak, biocDatasets, Biostrings, charm, ChIPpeakAnno, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, GenomicFeatures, GenomicRanges, GGtools, MEDIPS, methVisual, MotIV, 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.charm.hg18.example, pd.cytogenetics.array, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hg.u95a, pd.hg.u95av2, pd.ht.hg.u133.plus.pm, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pdInfoBuilder, PICS, R453Plus1Toolbox, rGADEM, rMAT, rnaSeqMap, Rolexa, Rsamtools, rtracklayer, segmentSeq, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Suggests Me	HilbertVis, HilbertVisGUI, oneChannelGUI, yeastRNASeq
Version	1.8.9
Since	Bioconductor 2.3 (R-2.8)

Package Downloads

Package Source	IRanges_1.8.9.tar.gz
Windows Binary	IRanges_1.8.9.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	IRanges_1.8.9.tgz
Package Downloads Report	Download Stats