DGE analysis on TCGA samples

[Arpita Mohapatra]

Good Morning, 

I want to perform DGE on selected subgroups, and I need to do that using DESeq2 method. I tried to change it in advanced options, but I don't see a DESeq2 option. 

I need the DESeq2 .csv file. 

can you advise on how I can do that? 

[Mary Goldman]

Good morning,

We automatically run DGE on our default datasets, which for most cohorts is not the counts data. DESeq2 requires counts data, which is why it is not shown as an option for FPKM, etc. I've added a feature request to run DGE on a non-default gene expression dataset. In the meantime, you can download our data and run the analysis on the Appyter site itself: https://appyters.maayanlab.cloud/#/Bulk_RNA_seq.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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