I am dealing with Whole-Genome-Bisulfite data and currently I am interested in DMRs. I have six tumor types and each tumor type has more than two subgroups. Since I would like to perform a intra- and inter-tumor analysis, a pairwise comparison for diff. methylated regions between tumors and groups within a tumor type is combinatorical not feasible. I search the web for solutions and found this paper, but the code, unfortunately, is not publicly available yet. Does anyone of you guys know a software package, which can detect DMRs in a mutligroup setting?
A example could look like: GBM vs. Medulloblastoma vs. ATRT vs. PA (for tumors)
Thanks for your help and best wishes,