charm

Analysis of DNA methylation data from CHARM microarrays

Bioconductor version: 2.8

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, Srinivasan Yegnasubramanian, 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

Details

biocViews Microarray, Bioinformatics, DNAMethylation
Depends R (>= 2.11.0), Biobase, SQN, fields, RColorBrewer, genefilter
Imports BSgenome, Biobase, oligo(>= 1.11.31), oligoClasses(>= 1.9.42), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils
Suggests charmData, BSgenome.Hsapiens.UCSC.hg18
System Requirements
License LGPL (>= 2)
URL
Depends On Me charmData
Imports Me
Suggests Me
Version 1.4.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source charm_1.4.0.tar.gz
Windows Binary charm_1.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary charm_1.4.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center