charm

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see charmData.

Analysis of DNA methylation data from CHARM microarrays


Bioconductor version: 3.6

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 (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("charm")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

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

Details

biocViews DNAMethylation, Microarray, Software
Version 2.24.0
In Bioconductor since BioC 2.6 (R-2.11) (14 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)
System Requirements
URL
See More
Suggests charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor
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Depends On Me charmData
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Package Archives

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

Source Package charm_2.24.0.tar.gz
Windows Binary charm_2.24.0.zip
Mac OS X 10.11 (El Capitan) charm_2.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/charm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/charm
Package Short Url https://bioconductor.org/packages/charm/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive