charm

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: Development (2.8)

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, Srinivasan Yegnasubramanian, Rafael Irizarry

Maintainer: Martin Aryee

To install this package, start R and enter:

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

Documentation

PDF

R Script

charm Vignette

Reference Manual

Details

biocViews	Microarray, Bioinformatics, DNAMethylation
Depends	R, Biobase, SQN, fields, RColorBrewer, genefilter
Imports	BSgenome, Biobase, oligo, oligoClasses, ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils
Suggests	charmData, BSgenome.Hsapiens.UCSC.hg18
System Requirements
License	LGPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version	1.3.6

Package Downloads

Package Source	charm_1.3.6.tar.gz
Windows Binary	charm_1.3.6.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	charm_1.3.6.tgz
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