DOI: 10.18129/B9.bioc.M3D    

Identifies differentially methylated regions across testing groups

Bioconductor version: Release (3.7)

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>

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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 1.14.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 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
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Source Package M3D_1.14.0.tar.gz
Windows Binary M3D_1.14.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan) M3D_1.14.0.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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