To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("charm")

In most cases, you don't need to download the package archive at all.

charm

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see charm.

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 3.2

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 jhu.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("charm")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("charm")
PDF charm Vignette
PDF Reference Manual
Text NEWS

Details

biocViews DNAMethylation, Microarray, Software
Version 2.16.1
In Bioconductor since BioC 2.6 (R-2.11) (6 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)
LinkingTo
Suggests charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor
SystemRequirements
Enhances
URL
Depends On Me charmData
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source charm_2.16.1.tar.gz
Windows Binary charm_2.16.1.zip
Mac OS X 10.6 (Snow Leopard) charm_2.16.0.tgz
Mac OS X 10.9 (Mavericks) charm_2.16.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/charm/tree/release-3.2
Package Short Url http://bioconductor.org/packages/charm/
Package Downloads Report Download Stats

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