To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

gmapR

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

Bioconductor version: Release (2.14)

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>

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

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 Alignment, Software
Version 1.6.6
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), GenomicFeatures, Biostrings, VariantAnnotation(>= 1.9.4), tools, Biobase, BSgenome, GenomicAlignments
Suggests RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, 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_1.6.6.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
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