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This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges.

Representation and manipulation of genomic intervals

Bioconductor version: 2.8

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: Biocore Team c/o BioC user list <bioconductor at>

Citation (from within R, enter citation("GenomicRanges")):


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PDF countGenomicOverlaps-decisiontree.pdf
PDF countGenomicOverlaps-genes.pdf
PDF countGenomicOverlaps.pdf
PDF GenomicRangesIntroduction.pdf
PDF GenomicRangesUseCases.pdf
PDF   Reference Manual


biocViews Annotation, Genetics, HighThroughputSequencing, Sequencing, Software
Version 1.4.8
In Bioconductor since BioC 2.6 (R-2.11) (6 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, IRanges(>= 1.10.6)
Imports methods, IRanges
LinkingTo IRanges
Suggests RUnit, BSgenome, GenomicFeatures, Rsamtools, EatonEtAlChIPseq(>= 0.0.2), leeBamViews, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2
Depends On Me BSgenome, cheung2010, chipseq, EatonEtAlChIPseq, GenomicFeatures, GGtools, PICS, Rsamtools, seqbias, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Imports Me ArrayExpressHTS, chipseq, ChIPseqR, GenomicFeatures, leeBamViews, PICS, rnaSeqMap, Rsamtools, rtracklayer, ShortRead, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Suggests Me
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