Representation and manipulation of genomic intervals

Bioconductor version: 2.9

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>

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


biocViews Genetics, Sequencing, HighThroughputSequencing, Annotation
Depends R (>= 2.8.0), methods, IRanges(>= 1.11.26)
Imports methods, IRanges
Suggests RUnit, BSgenome, GenomicFeatures, Rsamtools(>= 1.5.66), EatonEtAlChIPseq(>= 0.0.3), leeBamViews, edgeR, DESeq, rtracklayer, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2, DEXSeq, pasilla
System Requirements
License Artistic-2.0
Depends On Me BSgenome, cheung2010, chipseq, cn.mops, EatonEtAlChIPseq, exomeCopy, fastseg, GenomicFeatures, GGtools, ggtut, htSeqTools, PICS, Rsamtools, segmentSeq, seqbias, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, VariantAnnotation
Imports Me ArrayExpressHTS, biovizBase, chipseq, ChIPseqR, GenomicFeatures, genoset, ggbio, leeBamViews, nucleR, PICS, Repitools, rnaSeqMap, Rsamtools, rtracklayer, segmentSeq, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815
Suggests Me BeadArrayUseCases, Repitools
Version 1.6.7
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source GenomicRanges_1.6.7.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary GenomicRanges_1.6.7.tgz
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Fred Hutchinson Cancer Research Center