To install this package, start R and enter:

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

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

GenomicRanges

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges.

Representation and manipulation of genomic intervals

Bioconductor version: 2.12

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: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GenomicRanges")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicRanges")

PDF		An Introduction to GenomicRanges
PDF	R Script	GenomicRanges Use Cases
PDF	R Script	Overlap encodings
PDF	R Script	Overview of summarizeOverlaps
PDF		summarizeOverlaps-modes.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Sequencing, Software
Version	1.12.5
In Bioconductor since	BioC 2.6 (R-2.11) (6 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.5.4), IRanges(>= 1.17.33)
Imports	methods, utils, stats, BiocGenerics, IRanges
LinkingTo	IRanges
Suggests	AnnotationDbi(>= 1.21.1), Biostrings(>= 2.25.3), Rsamtools(>= 1.11.24), BSgenome, rtracklayer, GenomicFeatures, VariantAnnotation, edgeR, DESeq, DEXSeq, EatonEtAlChIPseq(>= 0.0.3), leeBamViews, pasilla, pasillaBamSubset, org.Sc.sgd.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, seqnames.db, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Dmelanogaster.UCSC.dm3, RUnit, digest
SystemRequirements
Enhances
URL
Depends On Me	annmap, biomvRCNS, BiSeq, BSgenome, bsseq, bumphunter, casper, cheung2010, chimera, chipseq, cn.mops, CSAR, DASiR, deepSNV, DESeq2, DiffBind, DREAM4, dsQTL, easyRNASeq, EatonEtAlChIPseq, ensemblVEP, epigenomix, exomeCopy, fastseg, genomes, GenomicFeatures, genoset, GGtools, ggtut, gmapR, gwascat, HiTC, htSeqTools, IlluminaHumanMethylation450kprobe, minfi, MMDiff, parathyroidSE, PING, QuasR, r3Cseq, Rcade, Repitools, RIPSeeker, Rsamtools, rSFFreader, RSVSim, rtracklayer, segmentSeq, seqbias, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SplicingGraphs, TransView, VariantAnnotation, VariantTools
Imports Me	AnnotationHub, ArrayExpressHTS, biovizBase, BiSeq, CAGEr, chipseq, ChIPseqR, copynumber, DESeq2, DEXSeq, epigenomix, FunciSNP, GenomicFeatures, genoset, ggbio, gmapR, Gviz, HTSeqGenie, HTSFilter, leeBamViews, MEDIPS, methyAnalysis, MethylSeekR, MinimumDistance, MMDiff, NarrowPeaks, nucleR, oligoClasses, PICS, prebs, QuasR, Repitools, rnaSeqMap, Rsamtools, rSFFreader, rtracklayer, segmentSeq, ShortRead, SNPchip, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SplicingGraphs, triplex, VanillaICE, VariantTools, waveTiling
Suggests Me	BeadArrayUseCases, BiocGenerics, IRanges, methylumi, MiRaGE, NarrowPeaks, Repitools, RnaSeqTutorial
Build Report

Package Archives

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

Package Source	GenomicRanges_1.12.5.tar.gz
Windows Binary	GenomicRanges_1.12.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GenomicRanges_1.12.5.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/GenomicRanges/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/GenomicRanges/
Package Downloads Report	Download Stats