scANVI

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# scANVI augments scVI to transfer cell type labelsimport anndataimport scvi
# read data and prepare for scvi-tools# adata contains partially observed cell type labels in adata.obs["labels"]# Unknown cells have the label "Unknown"adata = anndata.read("my_data.h5ad")scvi.data.setup_anndata(adata, batch_key="batch", labels_key="labels")model = scvi.model.SCANVI(adata, "Unknown")model.train()
# cell type predictionsadata.obs["predictions"] = model.predict()
# get integrated low-dimensional representationadata.obsm["X_scanvi"] = model.get_latent_representation()
# normalized expressionadata.layers["scanvi_norm"] = model.get_normalized_expression()
# differential expressionresults = model.differential_expression(    groupby="cell types",    group1="CD4",    group2="CD8")