scvi

scib.integration.scvi(adata, batch, hvg=None, return_model=False, max_epochs=None)

scVI wrapper function

Based on scvi-tools version >=0.16.0 (available through conda)

Note

scVI expects only non-normalized (count) data on highly variable genes!

Parameters:

  • adata – preprocessed anndata object

  • batch – batch key in adata.obs

  • hvg – list of highly variables to subset to. If None, the full dataset will be used

Returns:

anndata object containing the corrected feature matrix as well as an embedding representation of the corrected data