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 2.11 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges.

Representation and manipulation of genomic intervals

Bioconductor version: 2.11

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 1.10.7
In Bioconductor since BioC 2.6 (R-2.11) (6 years)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.1.12), IRanges(>= 1.15.42)
Imports methods, utils, BiocGenerics, IRanges
LinkingTo IRanges
Suggests Biostrings(>= 2.25.3), Rsamtools(>= 1.9.21), BSgenome, rtracklayer, GenomicFeatures, VariantAnnotation, edgeR, DESeq, DEXSeq, EatonEtAlChIPseq(>= 0.0.3), leeBamViews, pasilla, pasillaBamSubset, org.Sc.sgd.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Dmelanogaster.UCSC.dm3, RUnit, digest
SystemRequirements
Enhances
URL
Depends On Me annmap, BSgenome, bsseq, cheung2010, chipseq, cn.mops, CSAR, deepSNV, DiffBind, dsQTL, easyRNASeq, EatonEtAlChIPseq, exomeCopy, fastseg, genomes, GenomicFeatures, genoset, GGtools, ggtut, gmapR, gwascat, htSeqTools, minfi, PING, Rcade, Repitools, Rsamtools, rSFFreader, 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, TransView, VariantAnnotation, VariantTools
Imports Me ArrayExpressHTS, biovizBase, chipseq, ChIPseqR, FunciSNP, GenomicFeatures, genoset, ggbio, gmapR, Gviz, HTSeqGenie, leeBamViews, methyAnalysis, MinimumDistance, NarrowPeaks, nucleR, oligoClasses, PICS, 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, VanillaICE, VariantTools, waveTiling
Suggests Me BeadArrayUseCases, BiocGenerics, IRanges, MiRaGE, NarrowPeaks, Repitools, RnaSeqTutorial
Build Report

Package Archives

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

Package Source GenomicRanges_1.10.7.tar.gz
Windows Binary GenomicRanges_1.10.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomicRanges/tree/release-2.11
Package Short Url http://bioconductor.org/packages/GenomicRanges/
Package Downloads Report Download Stats

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