I am looking for a tool that can detect DMRs using the pairing information from normal-tumor samples. Looks like my study is kind of underpowered (because nobody asked me about the study design) and the only way to improve the power is to use all prior information. Do you know such callers? Really do not want to implement it myself...
The size of DMRs is of >=5kb, megabase-scale regions are also expected.
I've tried dmrseq, I like the method, but having 3 samples per group and 3 groups makes permutation approach (which is great in general) really underpowered...even if the regions are super long, their FDR are still higher than any reportable value