dealing with duplicated gene symbols
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- Dominant language
- Python
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Description
Hi Scanpy team!
After facing the issue with duplicated gene symbols again for the n-th time, I realised that one of the best solutions for renaming duplicates would likely be to do the following 'DuplicatedName-ENSEMBL_ID' rather than just adding an order-dependent number 'DuplicatedName-1' that can differ between dataset from different papers - preventing correct matching when integrating datasets which in turn essentially requires deleting duplicated genes.
What do you think in general?
Would it be possible to add support for this with interface like var_names_make_unique(unique_column='ENSEMBL')?
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 by locating the existing var_names_make_unique interface and reviewing how duplicated gene symbols and ENSEMBL identifiers are represented in integrated datasets. The issue names no files or tests; completion would require an agreed interface and deterministic naming behavior that can be checked across datasets.
Written by the indexing model from the issue text.
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