GenomicRanges

Representation and manipulation of genomic intervals

Bioconductor version: 2.7

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(>= 1.7.31)
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, GGtools, PICS, Rsamtools, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Imports Me	chipseq, ChIPseqR, GenomicFeatures, leeBamViews, PICS, Rsamtools, rtracklayer, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Suggests Me
Version	1.2.3
Since	Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source	GenomicRanges_1.2.3.tar.gz
Windows Binary	GenomicRanges_1.2.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	GenomicRanges_1.2.3.tgz
Package Downloads Report	Download Stats

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