Question: Differentially methylated regions Analysis
gravatar for David_emir
2.6 years ago by
David_emir380 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 • 1.3k views
ADD COMMENTlink modified 2.6 years ago by noorpratap.singh300 • written 2.6 years ago by David_emir380
gravatar for noorpratap.singh
2.6 years ago by
University of Maryland
noorpratap.singh300 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 2.6 years ago by noorpratap.singh300
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