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Questions tagged [gsea]

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2 votes
2 answers
2k views

Interpreting this plot from GSEA

I have RNA-seq for two groups of patients: Responders to chemotherapy (n=9) versus ...
Zizogolu's user avatar
  • 2,160
1 vote
2 answers
1k views

Ranking metric in GSEA

I am using fgsea in r to calculate and plot a bunch of GSEA graphs. My question is whether it is acceptable to use the Wald statistic from DeSeq2 to rank the gene list? I have seen in the GSEA ...
Jack Henry's user avatar
1 vote
3 answers
6k views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
beginner's user avatar
  • 631