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
objectbatch – 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