charm
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see charmData.
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>
citation("charm")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| charm Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Microarray, Software |
| Version | 2.29.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (14 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) |
| System Requirements | |
| URL |
See More
| Suggests | charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor |
| Linking To | |
| Enhances | |
| Depends On Me | charmData |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 [email protected]:packages/charm |
| Bioc Package Browser | https://code.bioconductor.org/browse/charm/ |
| Package Short Url | https://bioconductor.org/packages/charm/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |