Differentially methylated regions Analysis
Entering edit mode
4.7 years ago
David_emir ▴ 460

Hello All,

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,

Regards, Dave!

tcgabiolinks DMR packages • 1.9k views
Entering edit mode
4.7 years ago

Hi David, For RNA-Seq data use DESeq2. This is the most common package used for analysing RNASeq data and carrying differential analysis with a very helpful documentation and large community to help. For Methylation you can use minfi.

Hope it helps.


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