M3D: Identifies differentially methylated regions across testing groups

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("M3D")
AuthorTom Mayo
Bioconductor views Coverage CpGIsland DNAMethylation DifferentialMethylation
Date of publicationNone
MaintainerTom Mayo <t.mayo@ed.ac.uk>
LicenseArtistic License 2.0
Version1.10.0

View on Bioconductor

Functions

CpGsDemo Man page
determineGroupComps Man page
findComps Man page
M3D Man page
M3D-package Man page
M3D_Single Man page
M3D_Wrapper Man page
M3D_Wrapper_lite Man page
median_freq Man page
medianFreq Man page
MMDlistDemo Man page
PDemo Man page
plotCoverageSampleProfiles Man page
plotMethProfile Man page
plotMethSampleProfiles Man page
pvals Man page
pvals_lite Man page
readBedFiles Man page
readBedRaw Man page
rrbsDemo Man page
test_colData_structure Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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