navinlabcode / navinlabcode/CellTrek
Coembedding shows batch effect
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- Dominant language
- R
- Stars
- 135
- Forks
- 23
- PR merge metrics
- No merged PRs in 30d
Description
I obtained not very expected results from celltrek (some cell types are mapped randomly) and it made me wonder if something went wrong downstream. My main suspect is coembedding where data types are very well separated:
I followed the tutorial in the readme and did not apply any extra filtering/gene selection/preprocessing steps. Could you suggest what might be the issue?
Contributor guide
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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 by reproducing the README tutorial and inspect the coembedding step that produces the separated data types. Compare its inputs with the reported run and determine whether the batch effect explains the random cell-type mapping; done means identifying the cause or documenting the missing troubleshooting guidance.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100