Question about integrating unpaired data
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
- No merged PRs in 30d
Description
https://kzhang.org/SnapATAC2/tutorials/annotation.html
In this tutorial’s pipeline for annotating scATAC-seq data using scRNA-seq data, is it suitable for integrating unpaired scRNA-seq and scATAC-seq datasets? I’m currently doing this, but I’m unsure whether it’s a robust approach or if using a tool like GLUE (which is explicitly designed for unpaired data) would be more appropriate.
Additionally, is the data format generated by SnapATAC2 directly compatible with GLUE’s input requirements?
Contributor guide
No contributing guide indexed for this repository
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 at kzhang.org/SnapATAC2/tutorials/annotation.html, then review GLUE's documented input requirements and the SnapATAC2 data-export format. Done means documenting whether the tutorial supports unpaired scRNA-seq/scATAC-seq data and whether SnapATAC2 output can be used directly with GLUE.
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
- 25/100