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mahmoodlab / HEST

HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024
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Mapping gene names to Ensembl IDs #70

Open JosephDiPalma opened 2 days ago

JosephDiPalma commented 2 days ago

Did you have a chance to explore mapping the gene names to Ensembl IDs? I'm looking into that now and don't know if there's a recommended way.

guillaumejaume commented 2 days ago

As of today, we only provide support to de-alias HUGO gene names, https://github.com/mahmoodlab/HEST/blob/main/src/hest/HESTData.py#L1178.

@konst-int-i, do you have a code snipped to provide?

@JosephDiPalma, PR welcome! Handling gene names is always complex.

JosephDiPalma commented 2 days ago

I'll look into it further. Ultimately, I'd like to use it in something like Geneformer which requires the Ensembl IDs. Any further ideas would be appreciated too.

If I figure out a good solution, I'll send a PR.