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>

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

Installation

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


if (!require("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")
An Introduction to the M$^3$D method PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software
Version 1.22.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic License 2.0
Depends R (>= 3.3.0)
Imports parallel, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiSeq
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Suggests BiocStyle, knitr, testthat
Linking To Rcpp
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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/
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Old Source Packages for BioC 3.11 Source Archive