Glioblastoma subtype classification (ssGSEA)

[hye ryu]

For those of you who have ever conducted GBM classification, using  Wang's R package (  Tumor evolution of glioma intrinsic gene expression subtype associates with immunological changes in the microenvironment), I would appreiciate if you could help me. 

 I donwloaded the R function files, but I can't figure out how to run this. 

Especially, the data input format. I have a count matrix for bulk RNA sequence samples.  I am not really good with coding, so having a hard time understanding this source. 

https://rdrr.io/github/GSEA-MSigDB/GSEA_R/src/R/GSEA.GeneRanking.R

Thanks, 

Hye

[Anthony Castanza]

Hi Hye, 

You generally do not want to use the GSEA_R code, it is extremely old and no longer officially supported. We only continue to provide it for historical reproducibility and algorithmic research purposes. The current version of the GSEA application is available from our download page: https://www.gsea-msigdb.org/gsea/downloads.jsp

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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