Integration

Integration method functions require the preprocessed anndata object (here adata) and the name of the batch column in adata.obs (here 'batch'). The methods can be called using the following, where integration_method is the name of the integration method.

scib.ig.integration_method(adata, batch="batch")

For example, in order to run Scanorama, on a dataset, call:

scib.ig.scanorama(adata, batch="batch")

Warning

The following notation is deprecated.

scib.integration.runIntegrationMethod(adata, batch="batch")

Please use the snake_case naming without the run prefix.

Some integration methods (e.g. scgen(), scanvi()) also use cell type labels as input. For these, you need to additionally provide the corresponding label column of adata.obs (here cell_type).

scib.ig.scgen(adata, batch="batch", cell_type="cell_type")
scib.ig.scanvi(adata, batch="batch", labels="cell_type")

Functions

bbknn(adata, batch[, hvg])	BBKNN wrapper function
combat(adata, batch)	ComBat wrapper function (scanpy implementation)
desc(adata, batch[, res, ncores, tmp_dir, ...])	DESC wrapper function
mnn(adata, batch[, hvg])	MNN wrapper function (mnnpy implementation)
saucie(adata, batch)	SAUCIE wrapper function
scanorama(adata, batch[, hvg])	Scanorama wrapper function
scanvi(adata, batch, labels)	scANVI wrapper function
scgen(adata, batch, cell_type[, epochs, ...])	scGen wrapper function
scvi(adata, batch[, hvg])	scVI wrapper function
trvae(adata, batch[, hvg])	trVAE wrapper function
trvaep(adata, batch[, hvg])	trVAE wrapper function (pytorch implementatioon)