M3D

DOI: 10.18129/B9.bioc.M3D    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see M3D.

Identifies differentially methylated regions across testing groups

Bioconductor version: 3.11

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 "4.0") 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	1.22.0
In Bioconductor since	BioC 3.0 (R-3.1) (6 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
Links To Me
Build Report

Package Archives

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

Source Package	M3D_1.22.0.tar.gz
Windows Binary	M3D_1.22.0.zip (64-bit only)
macOS 10.13 (High Sierra)	M3D_1.22.0.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	https://bioconductor.org/packages/M3D/
Package Downloads Report	Download Stats