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Add differential expression #1295

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This PR adds the differential expression frontend plugin.

The differential expression plugin is intentionally copy/pasted from differential abundance. My two reasons for this are:

  1. Prevent accidentally breaking mbio during differential expression development
  2. The needs for this differential expression app are still evolving, and this path allows us the shortest time to a mvp while giving us space for that growth. If it turns out that in 6 months diff abund and diff expression are the same and we don't see them diverging any more, then we can go merge them together.

To run, you'll need a local eda backend. Rserve needs VEuPathDB/veupathUtils#50 installed, and we. need the add-differential-expression branch for service-eda. Alternatively, here's a screenshot of it working - there's not much to check :)

Screen Shot 2024-12-03 at 6 31 19 PM

Two things to note:

  1. Currently we can only test with mbio data. The backend has a temporary hack that transforms the loaded mbio data into what looks like RNA-Seq data.
  2. I left the collectionPredicate as true to allow all collections to be available in the app. We need to change this once we have real data to work with and we know what types of annotations we'll have.

@asizemore asizemore requested a review from dmfalke December 4, 2024 13:10
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I think your rationale for copying differential abundance makes sense. The layout of "Group Comparison" looks funny, in your screenshot, but I don't see anything specific to this PR that would cause that. Just wanted to mention it.

I haven't tested anything yet, but hope to soon. I suppose there isn't any harm in merging this, as the option won't show up until it's included in eda data.

@asizemore
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Excellent. Thanks @dmfalke ! I'll also look into that "Group Comparison" funky layout.

The backend has been merged, so we can now use the qa mbio site for testing. The backend currently will show this app for genomics (the intended user) and mbio (only used right now for testing because we dont have the genomcis data ready). So my current plan is to not merge this PR until I can update the backend and remove differential expression from mbio. We could probably have both merged but with irregular releases i don't want to miss something rolling out and accidentally taking this change with it!

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