charm

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: Release (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 jhsph.edu>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("charm")

Documentation

PDF R Script charm Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, Microarray, Software
Version 2.10.0
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 Downloads

Package Source charm_2.10.0.tar.gz
Windows Binary charm_2.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) charm_2.10.0.tgz
Mac OS X 10.9 (Mavericks)
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