cycombinepy.detect_batch_effect

cycombinepy.detect_batch_effect(adata, markers=None, batch_key='batch', sample_key='sample', downsample=None, out_dir=None, seed=472)

Comprehensive batch-effect diagnostic: express + UMAP + MAD summary.

Matches detect_batch_effect in R/detect_batch_effect.R.

Return type:

dict

Parameters:

• adata (AnnData)

• markers (Iterable[str] | None)

• batch_key (str)

• sample_key (str | None)

• downsample (int | None)

• out_dir (str | PathLike | None)

• seed (int)