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Add differential expression #1295
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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.
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! |
Just updated with |
Updated and fixed layout issue. Note, I directly copy/pasted the differential abundance css and it was quite painful to do so. I went back and forth between merging the two styles and sticking to the principle of separating new work from mbio work. The principle won in my head, but perhaps i've gone too far... |
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:
To run, you'll need a local eda backend. Rserve needs VEuPathDB/veupathUtils#50 installed, and we. need the
add-differential-expression
branch forservice-eda
. Alternatively, here's a screenshot of it working - there's not much to check :)Two things to note:
collectionPredicate
astrue
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.