MeDeCom is an R package for reference-free decomposition of heterogeneous DNA methylation profiles. It uses constrained matrix factorization enhanced by biologically-relevant constraints and a specially tailored regularization. See MeDeCom vignette for a more detailed description and an example analysis.
MeDeCom has originially been published in Genome Biology. Together with its accompanying packages DecompPipeline and FactorViz, MeDeCom is part of a published protocol for reference-free deconvolution of complex DNA methylation data (see also http://epigenomics.dkfz.de/DecompProtocol/).