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