gmapR
Provides convenience methods to work with GMAP and GSNAP from within R
Bioconductor version: Release (2.12)
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")
To cite this package in a publication, start R and enter:
citation("gmapR")
Documentation
| R Script | gmapR | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.11 (R-2.16) |
| 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, tools, Biobase, BSgenome |
| 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 Downloads
| Package Source | gmapR_1.2.0.tar.gz |
| Windows Binary | |
| Package Downloads Report | Download Stats |
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