GenomicRanges

Representation and manipulation of genomic intervals

Bioconductor version: 2.6

The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

Author: P. Aboyoun, H. Pages 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("GenomicRanges")

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

    citation("GenomicRanges")

Documentation

PDF		An Introduction to GenomicRanges
PDF	R Script	GenomicRanges Use Cases
PDF		Reference Manual

Details

biocViews	Genetics, Sequencing, HighThroughputSequencing, Annotation
Depends	R (>= 2.8.0), methods, IRanges(>= 1.5.74)
Imports	methods, IRanges
Suggests	RUnit, BSgenome, GenomicFeatures, Rsamtools, EatonEtAlChIPseq, leeBamViews, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2
System Requirements
License	Artistic-2.0
URL
Depends On Me	BSgenome, chipseq, GenomicFeatures, PICS, Rsamtools, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427
Imports Me	chipseq, ChIPseqR, GenomicFeatures, leeBamViews, PICS, Rsamtools, rtracklayer, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427
Suggests Me
Version	1.0.9
Since	Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source	GenomicRanges_1.0.9.tar.gz
Windows Binary	GenomicRanges_1.0.9.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	GenomicRanges_1.0.9.tgz
Package Downloads Report	Download Stats

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