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 3.3 of Bioconductor; for the stable, up-to-date release version, see gmapR.
An R interface to the GMAP/GSNAP/GSTRUCT suite
Bioconductor version: 3.3
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")
| R Script | gmapR | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (4 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_1.14.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.9 (Mavericks) | gmapR_1.14.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/gmapR/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/gmapR/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
