Question: Differentially methylated regions Analysis
gravatar for David_emir
17 months ago by
David_emir350 wrote:

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!

dmr packages tcgabiolinks • 824 views
ADD COMMENTlink modified 17 months ago by noorpratap.singh280 • written 17 months ago by David_emir350
gravatar for noorpratap.singh
17 months ago by
noorpratap.singh280 wrote:

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.

ADD COMMENTlink written 17 months ago by noorpratap.singh280
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1324 users visited in the last hour