To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gmapR")

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

gmapR

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see gmapR.

An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: 3.4

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:

## try http:// if https:// URLs are not supported
source("https://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 1.16.0
In Bioconductor since BioC 2.11 (R-2.15) (4.5 years)
License Artistic-2.0
Depends R (>= 2.15.0), methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.12), Rsamtools(>= 1.17.8)
Imports S4Vectors(>= 0.9.25), IRanges, rtracklayer(>= 1.31.2), GenomicFeatures(>= 1.17.13), Biostrings, VariantAnnotation(>= 1.11.4), tools, Biobase, BSgenome, GenomicAlignments(>= 1.1.9), BiocParallel
LinkingTo
Suggests RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
SystemRequirements
Enhances
URL
Depends On Me HTSeqGenie
Imports Me VariantTools
Suggests Me
Build Report

Package Archives

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

Package Source gmapR_1.16.0.tar.gz
Windows Binary
Mac OS X 10.9 (Mavericks) gmapR_1.16.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/gmapR/tree/release-3.4
Package Short Url http://bioconductor.org/packages/gmapR/
Package Downloads Report Download Stats

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