Provides convenience methods to work with GMAP and GSNAP from within R

Bioconductor version: Release (2.11)

GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.

Author: Cory Barr, Thomas Wu, Michael Lawrence

Maintainer: Cory Barr <barr.cory at>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script gmapR
PDF   Reference Manual


biocViews Software
Version 1.0.0
In Bioconductor since BioC 2.11 (R-2.15)
License Artistic-2.0
Depends R (>= 2.15.0), methods, GenomicRanges
Imports IRanges, Rsamtools(>= 1.7.4), rtracklayer(>= 1.17.15), GenomicRanges, GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase
Suggests RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
System Requirements
Depends On Me HTSeqGenie
Imports Me VariantTools
Suggests Me

Package Downloads

Package Source gmapR_1.0.0.tar.gz
Windows Binary
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