To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("M3D")
In most cases, you don't need to download the package archive at all.
M3D
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see M3D.
Identifies differentially methylated regions across testing groups
Bioconductor version: 3.3
This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.
Author: Tom Mayo
Maintainer: Tom Mayo <t.mayo at ed.ac.uk>
Citation (from within R,
enter citation("M3D")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("M3D")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("M3D")
| R Script | An Introduction to the M$^3$D method | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 years) |
| License | Artistic License 2.0 |
| Depends | R (>= 3.0.0) |
| Imports | BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiSeq, parallel |
| LinkingTo | |
| Suggests | BiocStyle, knitr, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | M3D_1.6.2.tar.gz |
| Windows Binary | M3D_1.6.2.zip |
| Mac OS X 10.9 (Mavericks) | M3D_1.6.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/M3D/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/M3D/ |
| Package Downloads Report | Download Stats |
Documentation »
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