omicverse.single.pySIMBA

omicverse.single.pySIMBA#

class omicverse.single.pySIMBA(adata, workdir='simba_result')[source]#

SIMBA wrapper for single-cell batch integration and graph-embedding construction.

Parameters:

  • adata (AnnData) – Input AnnData with batch labels in obs.

  • workdir (str, optional) – Directory used by SIMBA to store intermediate files and outputs.

Returns:

Initializes SIMBA runtime and stores input data/workspace.

Return type:

None

Examples

>>> simba_object = ov.single.pySIMBA(adata, workdir)
__init__(adata, workdir='simba_result')[source]#

Initialize SIMBA object for batch correction and multimodal analysis.

Parameters:

  • adata (anndata.AnnData) – Input AnnData containing single-cell profiles and batch labels.

  • workdir (str) – Working directory used by SIMBA for intermediate files.

Methods

__init__(adata[, workdir])

Initialize SIMBA object for batch correction and multimodal analysis.

batch_correction([use_precomputed])

Perform batch correction using the trained SIMBA model.

check_simba()

Check if SIMBA package has been installed.

gen_graph([n_components, k, copy, dirname])

Generate the graph structure for batch correction.

load([model_path])

Load a pre-trained SIMBA model for batch correction.

preprocess([batch_key, min_n_cells, method, ...])

Preprocess the AnnData object for SIMBA analysis.

train([num_workers, auto_wd, save_wd, output])

Train the SIMBA model for batch correction.
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