Using SCENIC+ with clustered and annotated anndataset
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
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Description
Hi,
Thank you for this amazing tool! I am working with snapATAC2 to do multi-sample analysis and have successfully processed the data and called peaks. I would like to do GRN analysis using SCENIC+ at this point. In the paper, it was mentioned that snapATAC2 integrate well with SCENIC+. I was wondering how that process would look like? SCENIC+ FAQs for Signac and ArchR indicate that completely processed data use, without modeling using pycisTopic, has not been tested before and is highly dependent on DAR calling. Therefore, I am confused.
Can I use marker regions as DARs here (obtained using tl.marker_regions) and the peak matrix? If yes, what would be a good substitution for Topics? Also, is there a function to convert the tl.motif_enrichment results to cistrome?
Thank you for your help!
Best,
Ananya
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First steps
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Research direction
Start by reviewing the SCENIC+, snapATAC2, pycisTopic, Signac, and ArchR workflow references mentioned in the issue. Check how tl.marker_regions, the peak matrix, and tl.motif_enrichment relate to DARs, topics, and cistromes. Done would require a documented, supported workflow or explicit guidance for this processed-data use case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100