Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 2.9

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 <aryee at>

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PDF R Script charm Vignette
PDF   Reference Manual
Text   NEWS


biocViews Microarray, Bioinformatics, DNAMethylation
Depends R (>= 2.11.0), Biobase, SQN, fields, RColorBrewer, genefilter
Imports BSgenome, Biobase, oligo(>= 1.11.31), oligoClasses(>= 1.9.42), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils
Suggests charmData, BSgenome.Hsapiens.UCSC.hg18
System Requirements
License LGPL (>= 2)
Depends On Me charmData
Imports Me
Suggests Me
Version 1.6.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source charm_1.6.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary charm_1.6.0.tgz
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