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ncborcherding / escape

Easy single cell analysis platform for enrichment
https://www.borch.dev/uploads/screpertoire/articles/running_escape
MIT License
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Error in runEscape #92

Closed BaluPai closed 6 months ago

BaluPai commented 6 months ago

Hi,

Thanks for this helpful tool for single-cell analysis! I have been recently trying Escape package following the nice tutorial: https://bioconductor.org/packages/release/bioc/vignettes/escape/inst/doc/vignette.html

But recently I tried to dig deeper, and wanted to try Normalization, additional visualization etc, like :https://www.borch.dev/uploads/screpertoire/articles/running_escape

Although I have installed escape and GSVA I am not able to use the function runEscape or escape.matrix !! Error in runEscape(object, method = "ssGSEA", gene.sets = GS.hallmark, : could not find function "runEscape" I also tried installing escape and gsva locally and calling it from local lib.

Any suggestions appreciated.

Best regards

ncborcherding commented 6 months ago

I see this issue is closed, but wanted to provide info for other users - this is likely a result of GSVA version. In preparation for a major overhaul in GSVA, escape requires GSVA v1.51.5 (not on Bioconductor 3.18). The easiest way to install is:

devtools::install_github("rcastelo/GSVA")

Nick

BaluPai commented 6 months ago

Thanks Nick for following up on this! Seems like there is also issues with Seurat v4 to v5 version too. I re-installed escape (1.99.1) and GSVA (1.51.9) on local PC and HPC server. I can access the runEscape/escape.matrix() functions. But seems 'enrichIt()' is not available with this version, is that right? I have few more queries regarding the normalization etc, which I would like to post later on separate thread. Best, Balu

ncborcherding commented 6 months ago

enrichIt() has been supersceded by runEscape() and escape.matrix() - still tracking down issues with v5