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Teichlab / celltypist

A tool for semi-automatic cell type classification
https://www.celltypist.org/
MIT License
278 stars 44 forks source link

Is celltypist suitable for predicting mouse immune types？ #127

Open ttt-404 opened 1 month ago

ttt-404 commented 1 month ago

Thank you for your amazing tool, but I wonder if “Immune_All_High/Low” models are suitable for predicting cell types in mouse data? I tried to do so, but only a few cell types (only 4/5 types) were provided, I wonder what's wrong... Thank you for your time if you can provide any information about this!

ChuanXu1 commented 1 month ago

@ttt-404, the immune model is from human, so very few genes are overlapped with your mouse data.

You can convert the human model to mouse one, and then apply CellTypist using the new model.

model = celltypist.Model.load('Immune_All_Low.pkl') model.convert() model.write('transformed_mouse_immune_model.pkl') celltypist.annotate(your_adata, model = 'transformed_mouse_immune_model.pkl', majority_voting = True)

The result should be interpreted with caution due to inter-species difference.