IRanges

Infrastructure for manipulating intervals on sequences

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

To install this package, start R and enter:

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

Documentation

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

Details

biocViews
Infrastructure , Genetics
Depends
R , methods , utils , stats
Imports
methods , utils , stats
Suggests
RUnit
System Requirements
License Artistic-2.0
URL
Depends On Me
BSgenome , BayesPeak , Biostrings , ChIPpeakAnno , GGtools , GenomicFeatures , GenomicRanges , Genominator , PICS , Rsamtools , ShortRead , VanillaICE , biocDatasets , chipseq , girafe , oneChannelGUI , rGADEM , rMAT , xmapcore
Imports Me
BayesPeak , Biostrings , ChIPpeakAnno , ChIPseqR , ChIPsim , ChromHeatMap , GGtools , GenomicFeatures , GenomicRanges , MotIV , PICS , Rolexa , Rsamtools , ShortRead , biocDatasets , charm , chipseq , methVisual , pdInfoBuilder , rGADEM , rMAT , rtracklayer , segmentSeq
Suggests Me
HilbertVisGUI , HilbertVis , oneChannelGUI

Package Downloads

Package source IRanges_1.6.16.tar.gz
Windows 32-bit binary IRanges_1.6.16.zip
Windows 64-bit binary IRanges_1.6.16.zip
MacOS X 10.5 (Leopard) binary IRanges_1.6.16.tgz
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