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.
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see charm.
Bioconductor version: 3.3
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("charm")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("charm")
R Script | charm Vignette | |
Reference Manual | ||
Text | NEWS |
biocViews | DNAMethylation, Microarray, Software |
Version | 2.18.0 |
In Bioconductor since | BioC 2.6 (R-2.11) (6.5 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 | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | charm_2.18.0.tar.gz |
Windows Binary | charm_2.18.0.zip |
Mac OS X 10.9 (Mavericks) | charm_2.18.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/charm/tree/release-3.3 |
Package Short Url | http://bioconductor.org/packages/charm/ |
Package Downloads Report | Download Stats |
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