GenomicRanges

Representation and manipulation of genomic intervals

Bioconductor version: 2.10

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

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Sequencing, Software
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.1.12), IRanges(>= 1.13.36)
Imports	methods, BiocGenerics, IRanges
Suggests	Rsamtools(>= 1.7.42), BSgenome, rtracklayer, GenomicFeatures, EatonEtAlChIPseq(>= 0.0.3), leeBamViews, edgeR, DESeq, rtracklayer, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2, DEXSeq, pasilla, pasillaBamSubset, VariantAnnotation, RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me	BSgenome, cheung2010, chipseq, cn.mops, CSAR, deepSNV, DiffBind, dsQTL, easyRNASeq, EatonEtAlChIPseq, exomeCopy, fastseg, GenomicFeatures, genoset, GGtools, ggtut, gwascat, htSeqTools, minfi, PICS, Repitools, Rsamtools, rtracklayer, segmentSeq, seqbias, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, VariantAnnotation
Imports Me	ArrayExpressHTS, biovizBase, chipseq, ChIPseqR, GenomicFeatures, genoset, ggbio, Gviz, leeBamViews, lumi, NarrowPeaks, nucleR, PICS, PING, Repitools, rnaSeqMap, Rsamtools, rtracklayer, segmentSeq, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119
Suggests Me	BeadArrayUseCases, BiocGenerics, NarrowPeaks, Repitools, RnaSeqTutorial
Version	1.8.13
Since	Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source	GenomicRanges_1.8.13.tar.gz
Windows Binary	GenomicRanges_1.8.13.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	GenomicRanges_1.8.13.tgz
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