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>

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


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


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
Depends On Me
Imports Me
Suggests Me
Links To Me
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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/
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