ssGSEA 2.0 R Package?
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10 months ago
ivanarg2 ▴ 80

Hi all. I've recently ran into some trouble using the GSVA package for running ssGSEA (i.e., gsva(data, pathways, method = 'ssGSEA'). Googling a bit revealed a new ssGSEA 2.0 provided by Broad under their Gene Pattern module (see https://github.com/broadinstitute/ssGSEA2.0 and https://gsea-msigdb.github.io/ssGSEA-gpmodule/v10/index.html), and I wonder whether using this new and improved version of ssGSEA will magically resolve my issues.

However, I don't see a ready-made package that I could easily use in RStudio. Does anyone know how to run ssGSEA2.0 / ssGSEA v10 in RStudio? Can I download anything from the GitHub for this purpose?

Many thanks

ssGSEA R • 1.5k views
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The first Github link has explicit instructions. I'd recommend trying them. In all likelihood, you will run into the same issue, so resolving that will likely be the only real solution.

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You're probably right, but it's worth a shot. Regarding GitHub, I tried following their instructions, but given that I've never used GitHub before, and that I only use packages from CRAN/BioConductor, I don't know how to implement their instructions. Currently, I'm getting the following error when I try to 'source' their ssgsea-cli.R file: Error in file(filename, "r", encoding = encoding) : cannot open the connection

I've extracted all the files in the GitHub to a director, and set my working dir to this location.

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Note: the GUI version works, but I can't use RStudio commands to do a batch of 20 analyses

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Well, the CLI script is meant to be use from the command line. If you want to use the function directly, then you need to source these files and read the ssGSEA2.0.R script to determine the ssGSEA2 function parameters.

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Got it. I thought the CLI was meant to be used with RStudio commands, but I see that I misinterpreted that. I'll give your advice a shot, and if it doesn't work I'll go back to the original GSVA function and figure out the core issue. Thx for the tips.

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