Suggestions on running copykat for multiple samples without cell type annotation?
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 15/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
This issue names no files, tests, or entry points. Start by reviewing CopyKAT's existing usage documentation for multi-sample matrices and cell-type annotation; the work is done when both questions have documented, project-supported answers, including how to handle batch effects and identify normal and tumor cells.
Written by the indexing model from the issue text.
Description
Hi, I have two questions regarding copykat:
- is it recommended to run copyKat for a merged count matrix from multiple samples? If so, how do you deal with batch effects?
- Can I run copykat without annotating cell types? What is the best strategy to identify normal and tumor cells using this tool?
- Dominant language
- R
- Stars
- 305
- Forks
- 66
- PR merge metrics
- No merged PRs in 30d
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.
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