charm

DOI: 10.18129/B9.bioc.charm    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see charm.

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 3.9

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>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	charm Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Microarray, Software
Version	2.29.0
In Bioconductor since	BioC 2.6 (R-2.11) (9.5 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
Links To Me
Build Report

Package Archives

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

Source Package	charm_2.29.0.tar.gz
Windows Binary	charm_2.29.0.zip
Mac OS X 10.11 (El Capitan)	charm_2.29.0.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