Representation and manipulation of genomic intervals

Bioconductor version: Release (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>

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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


biocViews Annotation, Genetics, HighThroughputSequencing, Sequencing, Software
Version 1.10.7
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.1.12), IRanges(>= 1.15.42)
Imports methods, utils, BiocGenerics, 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
System Requirements
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, 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

Package Downloads

Package Source GenomicRanges_1.10.7.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) GenomicRanges_1.10.7.tgz
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