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. ~scib.integration.scgen, ~scib.integration.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")scib.integration
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runBBKNN
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runCombat
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runMNN
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runDESC
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runSaucie
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runScanorama
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runScanvi
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runScGen
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runScvi
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runTrVae
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runTrVaep
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issparse