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.
Bioconductor version: 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")
):
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("gmapR")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gmapR")
R Script | gmapR | |
Reference Manual | ||
Text | NEWS |
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 |
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) | |
Browse/checkout source | (username/password: readonly) |
Package Downloads Report | Download Stats |
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