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bowang-lab / scGPT

https://scgpt.readthedocs.io/en/latest/
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Cell type annotation tutorial together with multiomics tutorial. #120

Closed Ragagnin closed 11 months ago

Ragagnin commented 11 months ago

Hello, congratulations on the excellent work!

I'm trying to use the multiomics tutorial together with the cell type annotation tutorial to predict cell types through multiomics data.

I'm having some difficulties putting the two tutorials together.

Do you have any tips or step-by-step instructions for carrying out this particular task?

Thank you very much in advance!

subercui commented 11 months ago

Hi, thank you for the question! That would be interesting, one straight-forward idea I have is to use the classification training pipeline in the annotation tutorial while using the multi-omics data processing and model settings. Please note the current annotation tutorial assumes you have some "reference" data that has been annotated, and will train a classifier on these data and apply it to the actual query data. Is this what you need?

BTW, I just saw your original discussion #116, shall we close this issue and continue the discussion there?

Ragagnin commented 11 months ago

Of course, we can follow this topic on discussions.

"Please note the current annotation tutorial assumes you have some "reference" data that has been annotated, and will train a classifier on these data and apply it to the current query data. Is this what you need?"

Exactly! I have a database as a reference.

Thank you for your support!