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Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 2.14

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>

Citation (from within R, enter citation("charm")):


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PDF R Script charm Vignette
PDF   Reference Manual
Text   NEWS


biocViews DNAMethylation, Microarray, Software
Version 2.10.1
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
Depends On Me charmData
Imports Me
Suggests Me

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Package Source charm_2.10.1.tar.gz
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Mac OS X 10.6 (Snow Leopard) charm_2.10.1.tgz
Mac OS X 10.9 (Mavericks) charm_2.10.1.tgz
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