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 <method>
is the name of the integration method.
scib.ig.<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.run<method>(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 wrapper function |
|
ComBat wrapper function ( |
|
DESC wrapper function |
|
MNN wrapper function ( |
|
SAUCIE wrapper function |
|
Scanorama wrapper function |
|
scANVI wrapper function |
|
scGen wrapper function |
|
scVI wrapper function |
|
trVAE wrapper function |
|
trVAE wrapper function ( |