AlexsLemonade / AlexsLemonade/scpcaTools

Ensure imported barcodes have no zero counts

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#287 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
Stars
1
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0
PR merge metrics
No merged PRs in 30d

Description

In https://github.com/AlexsLemonade/scpcaTools/pull/286 we updated the alevin-fry import to round counts when requested, but in doing so we can sometimes create SCE objects where there is a barcode with all zero counts. We should filter these out to avoid some potential downstream issues.

Contributor guide

Open the contributing guide

Research direction

Start by reviewing pull request #286 and the alevin-fry import path it changed. Update the import behavior so resulting SCE objects exclude barcodes with all zero counts, then verify imported objects contain no all-zero barcodes.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
50/100

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