daisybio / daisybio/SPONGE

SPONGEffects enrichment_modules uses outdated software

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Dominant language
R
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Description

This function of SPONGEffects uses outdated software from the `GSVA` package.
Since Bioconductor 3.18 this has changed (copied from [documentation](https://www.rdocumentation.org/packages/GSVA/versions/1.20.0)):

Instead of gsva(expr=., gset.idx.list=., method=., ...), use a method-specific parameter object, see [plageParam](http://127.0.0.1:38211/help/library/GSVA/help/plageParam) [zscoreParam](http://127.0.0.1:38211/help/library/GSVA/help/zscoreParam) [ssgseaParam](http://127.0.0.1:38211/help/library/GSVA/help/ssgseaParam) [gsvaParam](http://127.0.0.1:38211/help/library/GSVA/help/gsvaParam), followed by a call to the new gsva() function, see [gsva](http://127.0.0.1:38211/help/library/GSVA/help/gsva).

Probably the corresponding function in `SPONGE::enrichment_modules()` has to be replaced, the functionality should be identical.

Contributor guide

No contributing guide indexed for this repository

Research direction

Locate SPONGE::enrichment_modules() and compare its GSVA call with the linked GSVA documentation for Bioconductor 3.18. Verify the replacement preserves the existing enrichment functionality and outputs, then test the function with the project's available checks or examples.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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