To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rMAT")
In most cases, you don't need to download the package archive at all.
rMAT
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
Bioconductor version: 3.0
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 (from within R,
enter citation("rMAT")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rMAT")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rMAT")
| R Script | The rMAT users guide | |
| Reference Manual |
Details
| biocViews | Microarray, Preprocessing, Software |
| Version | 3.16.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) |
| 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 |
| LinkingTo | |
| Suggests | GenomeGraphs, rtracklayer |
| SystemRequirements | |
| Enhances | |
| URL | http://www.rglab.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rMAT_3.16.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | rMAT_3.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | rMAT_3.16.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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