M3D

DOI: 10.18129/B9.bioc.M3D    

This is the development version of M3D; for the stable release version, see M3D.

Identifies differentially methylated regions across testing groups

Bioconductor version: Development (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>

Citation (from within R, enter citation("M3D")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("M3D")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software
Version 1.21.0
In Bioconductor since BioC 3.0 (R-3.1) (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
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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

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