Could data from UCSC Xena used as an input for PyDESeq2?

[fredsamhaak]

Hi, thanks for your great job. I am going to do DEA based on data downloaded from UCSC Xena:

I wonder if PyDESeq2 could deal with these data (e.g. RSEM expected_count (DESeq2 standardized)). Is 'raw read count' strictly needed as an input for PyDESeq2?

Thanks in advance and really looking forward to hearing from you.

[abearab]

I think you can assume data is already normalized and use pyDESeq2 for differential expression analysis skipping normalization step.

This tutorial can help you understand analysis steps and logical reasoning for each step.

https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html