source("http://bioconductor.org/biocLite.R")
biocLite("gmapR")

gmapR

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

Bioconductor version: 2.13

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: Michael Lawrence <lawrence.michael at gene.com>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("gmapR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gmapR")

 

PDF	R Script	gmapR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software
Version	1.4.3
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(>= 1.7.34), tools, Biobase, BSgenome, methods
Suggests	RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
System Requirements
URL
Depends On Me	HTSeqGenie
Imports Me	VariantTools
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	gmapR_1.4.3.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
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