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 stat.math.ethz.ch>

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 countGenomicOverlaps-decisiontree.pdf
PDF countGenomicOverlaps-genes.pdf
PDF R Script Counting Alignment Overlaps with countGenomicOverlaps
PDF R Script GenomicRanges Use Cases
PDF   Reference Manual

Details

biocViews Genetics, Sequencing, HighThroughputSequencing, Annotation
Depends R (>= 2.8.0), methods, IRanges(>= 1.10.6)
Imports methods, IRanges
Suggests RUnit, BSgenome, GenomicFeatures, Rsamtools, EatonEtAlChIPseq(>= 0.0.2), leeBamViews, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2
System Requirements
License Artistic-2.0
URL
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
Version 1.4.8
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source GenomicRanges_1.4.8.tar.gz
Windows Binary GenomicRanges_1.4.8.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary GenomicRanges_1.4.8.tgz
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