AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Consider using a converted Seurat object in hello-clusters

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Description

For https://github.com/AlexsLemonade/OpenScPCA-nf/issues/108, we are working towards offering Seurat-ified processed ScPCA files as part of OpenScPCA results.
In this `hello-clusters` notebook, we convert an SCE to Seurat using `rOpenScPCA`. We might consider just reading in the Seurat file version directly, although this would mean there's an additional dependency to download those results files in this module. I'm opening this issue to both a) decide if we want to read in from results, and if so b) update notebook accordingly.

https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/77b6f7719dfa979a5de11ade793518a61316b026/analyses/hello-clusters/01_perform-evaluate-clustering.Rmd#L332-L348

Contributor guide

Open the contributing guide

Research direction

Review issue #108 and the linked section of analyses/hello-clusters/01_perform-evaluate-clustering.Rmd at lines 332-348. Decide whether hello-clusters should read the converted Seurat results directly, considering the additional dependency for downloading them. Done means the decision is recorded and the notebook is updated if direct reading is chosen.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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