gsea function

[summer-yangqin]

Hello,
When I run the R script bulkRNASeq_survival_analysis.R, there is a question. which package is used for the function of gsea?
"gsea(signature = x, geneset =g, twoTails = F, pout = TRUE, per = 1000, colSig = c(.15,0.45, 0.3, 1), colHit = c(.05,0.58, 0.1, 2)) "
Thanks !

[Aleksobrad]

Thank you for the questions-- we actually use a package called atools widely shared within the Califano Lab. It performs gsea as described in the methods section. For convenience I have added the package folder as "atools.zip" directly to https://github.com/Aleksobrad/single-cell-rcc-pipeline

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On Tue, Jul 20, 2021 at 4:46 AM qinqinyang ***@***.***> wrote: Hello, When I run the R script bulkRNASeq_survival_analysis.R, there is a question. which package is used for the function of gsea? "gsea(signature = x, geneset =g, twoTails = F, pout = TRUE, per = 1000, colSig = c(.15,0.45, 0.3, 1), colHit = c(.05,0.58, 0.1, 2)) " Thanks ! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLHK2WYEH4HYM35R5WSZ43TYUZU3ANCNFSM5AVK3O6Q> .

[summer-yangqin]

Thank you for the fast and kind reply!