omicverse.single.lazy

omicverse.single.lazy(adata, species='human', reforce_steps=[], sample_key=None, qc_kwargs=None, preprocess_kwargs=None, pca_kwargs=None, harmony_kwargs=None, scvi_kwargs=None)[source]

Run a one-click single-cell analysis pipeline with resumable steps.

Parameters:

  • adata (AnnData) – Input AnnData to be processed.

  • species (str) – Species name used by downstream annotation helpers.

  • reforce_steps (list) – Step names forced to rerun even if status flags exist. Common values: ['qc', 'pca', 'preprocess', 'scaled', 'Harmony', 'scVI', 'eval_bench', 'eval_clusters'].

  • sample_key (str or None) – Column in adata.obs used as batch key for correction/integration.

  • qc_kwargs (dict or None) – Keyword arguments passed to ov.pp.qc.

  • preprocess_kwargs (dict or None) – Keyword arguments passed to ov.pp.preprocess.

  • pca_kwargs (dict or None) – Keyword arguments passed to PCA routine.

  • harmony_kwargs (dict or None) – Keyword arguments for Harmony integration block.

  • scvi_kwargs (dict or None) – Keyword arguments for scVI integration block.

Returns:

Updated AnnData with QC, preprocessing, embeddings, and clustering results.

Return type:

AnnData