gmapR

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

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

Documentation

PDF R Script gmapR
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Software
Version 1.7.5
In Bioconductor since BioC 2.11 (R-2.15)
License Artistic-2.0
Depends R (>= 2.15.0), methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.12)
Imports S4Vectors, IRanges, Rsamtools(>= 1.17.8), rtracklayer(>= 1.25.5), GenomicFeatures, Biostrings, VariantAnnotation(>= 1.11.4), tools, Biobase, BSgenome, GenomicAlignments(>= 1.1.9)
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 Downloads

Package Source gmapR_1.7.5.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
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