charm

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 2.10

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: Martin Aryee <aryee at jhu.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 Bioinformatics, DNAMethylation, Microarray, Software
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
System Requirements
License LGPL (>= 2)
URL
Depends On Me charmData
Imports Me
Suggests Me
Version 2.2.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source charm_2.2.0.tar.gz
Windows Binary charm_2.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary charm_2.2.0.tgz
Package Downloads Report Download Stats

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