scanvi

scib.integration.scanvi(adata, batch, labels, hvg=None, max_epochs=None)

scANVI wrapper function

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

Note

Use non-normalized (count) data for scANVI!

Parameters:

  • adata – preprocessed anndata object

  • batch – batch key in adata.obs

  • labels – label 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