How to score cluster for presence of marker genes?
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- Dominant language
- Python
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Description
A frequent problem that I am faced with is to identify clusters using known lists of markers. I think that one existing approach is to first identify markers and then check if the known markers are among those identified markers. Also, I have used the score_genes function, originally used to identify cell cycle genes. However, I think that a more robust method is possible and probably I am just not aware of it. Does anyone has some experience with this?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by reviewing the existing score_genes function and the marker-identification approach described in the issue. Define the desired scoring behavior for known marker lists and cluster results; the payload identifies no target file or test, so completion would require an agreed method and validation plan.
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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
- 25/100