M3D

DOI: 10.18129/B9.bioc.M3D    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see M3D.

Identifies differentially methylated regions across testing groups

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("M3D")

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("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	1.16.0
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 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
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	M3D_1.16.0.tar.gz
Windows Binary	M3D_1.16.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan)	M3D_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/M3D
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/M3D
Package Short Url	http://bioconductor.org/packages/M3D/
Package Downloads Report	Download Stats