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Aleksobrad / single-cell-rcc-pipeline

Data files and code for analysis of single-cell ccRCC data for the manuscript "Tumor-Specific Cell Populations in Clear Cell Renal Carcinoma Associated with Clinical Outcome Identified Using Single-Cell Protein Activity Inference." Includes code for VIPER protein activity inference pipeline
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gsea function #4

Open summer-yangqin opened 3 years ago

summer-yangqin commented 3 years ago

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 commented 3 years ago

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

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 !

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summer-yangqin commented 3 years ago

Thank you for the fast and kind reply!