M3D 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
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M3D: a kernel-based test for spatially correlated changes in methylation profiles.
Mayo T, Schweikert G, Sanguinetti G.
Bioinformatics. 2014 Nov 13. pii: btu749.