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

 

   

Identifies differentially methylated regions across testing groups

Bioconductor version: Release (3.5)

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")

 

PDF R Script An Introduction to the M$^3$D method
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software
Version 1.10.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License Artistic License 2.0
Depends R (>= 3.3.0)
Imports parallel, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiSeq
LinkingTo Rcpp
Suggests BiocStyle, knitr, testthat
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_1.10.0.tar.gz
Windows Binary M3D_1.10.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan) M3D_1.10.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/M3D/tree/release-3.5
Package Short Url http://bioconductor.org/packages/M3D/
Package Downloads Report Download Stats

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