I have TCGA data from RNAseq(Counts data) and DNA-Meth data. I am interested to conduct Differentially methylated regions Analysis on the same. I have tried working with TCGABioLinks package, and I am finding it difficult to execute and understand as well. After wasting about 2 months on it now I have decided to dump this less friendly package and move on (Sad, I have invested so much time in this package). My question is, other than TCGAbiolinks do I have any other option/s for conducting Differentially methylated regions Analysis/ Differentially Expression analysis of TCGA data? Please help me in identifying a suitable package which can be used by a biologist, with less experience in hardcoding.
Thanks a lot for your help,