How to create scANVI model from a scVI model without labels_key?

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1

I had not set labels_key when first using. sca.models.SCVI.setup_anndata(source_adata,batch_key=condition_key). After annotated all cells, how could I create a scANVI model with the first scVI model? Or, should I just try to train a new scVI model with ‘labels_key’.

2

Hi, we have an example of that in this tutorial, where you can set a new labels key for scANVI after training with scVI.

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3

Thanks so much, it is useful when using scarches same as scvi-tools.