DOI: 10.18129/B9.bioc.charm    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: Release (3.10)

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")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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biocViews DNAMethylation, Microarray, Software
Version 2.32.0
In Bioconductor since BioC 2.6 (R-2.11) (10 years)
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
Depends On Me charmData
Imports Me
Suggests Me
Links To Me
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