rMAT
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see rMAT.
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
Bioconductor version: 3.9
This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!
Author: Charles Cheung and Arnaud Droit and Raphael Gottardo
Maintainer: Arnaud Droit <arnaud.droit at crchuq.ulaval.ca> and Raphael Gottardo <rgottard at fhcrc.org>
citation("rMAT")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rMAT")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rMAT")| The rMAT users guide | R Script | |
| Reference Manual |
Details
| biocViews | Microarray, Preprocessing, Software |
| Version | 3.33.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (15 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.9.0), BiocGenerics(>= 0.1.3), IRanges(>= 1.13.10), Biobase(>= 2.15.1), affxparser |
| Imports | stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4 |
| System Requirements | GSL (GNU Scientific Library) |
| URL | http://www.rglab.org |
See More
| Suggests | GenomeGraphs, rtracklayer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rMAT_3.33.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | rMAT_3.33.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rMAT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rMAT |
| Bioc Package Browser | https://code.bioconductor.org/browse/rMAT/ |
| Package Short Url | https://bioconductor.org/packages/rMAT/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |