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Move differential expression analysis to separate package #730

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grst opened this issue Mar 19, 2025 · 2 comments
Open

Move differential expression analysis to separate package #730

grst opened this issue Mar 19, 2025 · 2 comments
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enhancement New feature or request

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@grst
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grst commented Mar 19, 2025

Description of feature

After factoring out the differential expression visualizations into deres, I've been thinking if it would also make sense to make a separate package for the differential expression testing altogether.

It's useful in many contexts (e.g. differential spatial analysis) as we've seen during the hackathon and I would like to have that available to the scverse ecosystem without the hefty dependency tree pertpy brings with it.

The new package (e.g. demodels) could then become a dependency of pertpy and the corresponding class definitions could be re-rexported in the pertpy API such that there are no user-facing changes.

LMK what you think @Zethson.

@grst grst added the enhancement New feature or request label Mar 19, 2025
@maltekuehl
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I support this idea which seems to align with how I personally would use pertpy, which would largely just be for differential expression. Typical pertpy applications as initially conceptualized might also not directly benefit from the implementation of additional statistical testing features (e.g., more test statistics, flexibilizing existing APIs to offer a more modular composability, etc.) but other packages might and in my opinion it could make sense to unlink the development processes and feature sets. If this were to be of interest, I would be happy to help with the development of the outsourced package.

@Zethson
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Zethson commented Mar 24, 2025

Totally fine with me as long as there are no user facing changes (for now). Making pertpys dependencies leaner is still an achievable goal of mine but I am overloaded for the next few months.

+1!

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