Use multiple groups as reference when testing genes
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Nobody has claimed this yet.
Area – Differential Expression
- Dominant language
- Python
- Stars
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
When testing for differential genes among groups with rank_genes_groups function, two options are available for reference: 'rest' or any other single group. It would be helpful to have the possibility to choose different groups as reference (reference: Union[Literal['rest'], Iterable[str]] = 'rest').
Contributor guide
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 at the rank_genes_groups function and trace how its current reference values are handled. Determine how multiple named groups should be accepted as a reference and verify that the resulting differential-gene testing behavior matches the requested semantics.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100