Gene Symbols from Ensembl or custom source + better handling of identifiers and orthology translation

saezlab / decoupler-py

Python package to perform enrichment analysis from omics data.

https://decoupler-py.readthedocs.io/

GNU General Public License v3.0

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Gene Symbols from Ensembl or custom source + better handling of identifiers and orthology translation #121

Closed deeenes closed 1 month ago

deeenes commented 1 month ago

Hi @PauBadiaM,

Here I implemented the stuff that the email discussion was about, now the user has 5 choices:

Use the gene symbols from the web service (the original behaviour)
Update them from Ensembl
Update them from UniProt
Provide a dict[str, set[str]] with any custom mapping
Use UniProt IDs instead of gene symbols

I checked all omnip.get_* functions with various options, and everything looks alright for me. If you agree, feel free to merge this to main.

deeenes commented 1 month ago

That particular error I've just fixed in pypath a few days ago; however, I expect another error due to OMA API change, that too will be fixed very soon.