source("http://bioconductor.org/biocLite.R")
biocLite("charm")

charm

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 2.13

This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.

Author: Martin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry

Maintainer: Peter Murakami <pmurakam at jhsph.edu>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("charm")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("charm")

 

PDF	R Script	charm Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, DNAMethylation, Microarray, Software
Version	2.8.0
In Bioconductor since	BioC 2.6 (R-2.11)
License	LGPL (>= 2)
Depends	R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter
Imports	BSgenome, Biobase, oligo(>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2)
Suggests	charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor
System Requirements
URL
Depends On Me	charmData
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	charm_2.8.0.tar.gz
Windows Binary	charm_2.8.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	charm_2.8.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats