charm

DOI: 10.18129/B9.bioc.charm    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of charm; to use it, please install the devel version of Bioconductor.

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: Development (3.10)

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: Peter Murakami <pmurakam at jhu.edu>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("charm")

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

Documentation

PDF   Reference Manual

Details

biocViews DNAMethylation, Microarray, Software
Version 2.31.1
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
Windows Binary
Mac OS X 10.11 (El Capitan)
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/
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