GenomicRanges

Representation and manipulation of genomic intervals

Bioconductor version: Release (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>

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	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)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.5.4), IRanges(>= 1.17.33)
Imports	methods, utils, stats, BiocGenerics, 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
System Requirements
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

Package Downloads

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
Package Downloads Report	Download Stats

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