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Single-cell Variational Inference

This page is under construction. For now, please learn more about scVI in our user guide.

# scVI is for end-to-end analysis of scRNA-seq dataimport anndataimport scvi
# read data and prepare for scvi-toolsadata = anndata.read("my_data.h5ad")scvi.data.setup_anndata(adata, batch_key="batch")model = scvi.model.SCVI(adata)model.train()
# get integrated low-dimensional representationadata.obsm["X_scvi"] = model.get_latent_representation()
# normalized expressionadata.layers["scvi_norm"] = model.get_normalized_expression()
# differential expressionresults = model.differential_expression(    groupby="cell types",    group1="CD4",    group2="CD8")