Label Transfer Using the SCVI-tools
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
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Description
Hello. Thank you for this package. I'm doing an integration analysis using more than 40 scATAC samples. However, I do not have scRNA data from the same cells. I tried doing the label transfer using the SCVI-tools as you demonstrated here: https://kzhang.org/SnapATAC2/tutorials/annotation.html
The RNA-seq data I'm using is from the same disease model, but the cells are not overlapping at all.
It looks like this:
Do you have any suggestions to improve the label transferring?
Do you have any plans of adding the FindTransferAnchors function from the Seurat package or do you think it is a better approach?
Thank you.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the annotation tutorial linked in the issue and reproduce the SCVI-tools label-transfer workflow on the stated non-overlapping scRNA/scATAC data. Then evaluate the requested Seurat FindTransferAnchors approach and document whether support or guidance is appropriate; done means a reproducible recommendation or a scoped implementation plan.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100