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YosefLab / PopV

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Missing Kidney reference from Zenodo record (KeyError: 'Kidney') #45

Closed olivermccallion closed 2 days ago

olivermccallion commented 9 months ago

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Hi,

Thanks for producing this package. In the listed tissue options there is a 'Kidney' reference but this is not in the Zenodo reference record https://zenodo.org/api/records/7587774. I therefore get a KeyError when the tissue type is set to 'Kidney'. Is the kidney reference available and if so could the reference be updated or could you provide a link? I tried https://zenodo.org/api/records/7580707/files/pretrained_models_Kidney_ts.tar.gz/content

Thanks Oliver

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canergen commented 9 months ago

Thanks for the pointer. IMO we don't have a high quality kidney dataset in Tabula sapiens (it's difficult to obtain kidney tissue from organ donations). I would recommend using https://www.kidneycellatlas.org and retrain the classifiers. I still need to fix the notebook in that regard.

canergen commented 2 days ago

Tabula sapiens v2 will also contain a kidney reference. Publication is around the corner and we will update all models once ready.