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.
charm
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see 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>
Citation (from within R,
enter citation("charm")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("charm")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("charm")
| charm.pdf | ||
| Reference Manual |
Details
| biocViews | Bioinformatics, DNAMethylation, Microarray, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (6 years) |
| License | LGPL (>= 2) |
| 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 |
| LinkingTo | |
| Suggests | charmData, BSgenome.Hsapiens.UCSC.hg18 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | charmData |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | charm_1.4.0.tar.gz |
| Windows Binary | charm_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/charm/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/charm/ |
| Package Downloads Report | Download Stats |
Documentation »
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