scatrans.active_score_simple

scatrans.active_score_simple#

scatrans.active_score_simple(adata_input, groupby='condition', target_group='Disease', reference_group='Control', sample_col=None, organism='mouse', *, show_plot=False, copy_input=True, pydeseq2_min_counts=10)[source]#

Recommended entry point for new users (minimal parameters).

Wraps active_score() with sensible defaults: - Uses “Disease”/”Control” as group defaults (unlike core active_score which defaults

to the historical “GA”/”Ctrl”).

  • heuristic mode, no permutation (inspect all_results + filter_active_genes)

  • auto-attaches bundled gene features when missing

  • pseudobulk + PyDESeq2 when sample_col has >=3 replicates per group; otherwise single-cell Wilcoxon DE

For full control (permutation, advanced mode, mixed models, etc.) use active_score() directly.

Parameters:

  • adata_input (Any)

  • groupby (str)

  • target_group (str)

  • reference_group (str)

  • sample_col (str | None)

  • organism (str)

  • show_plot (bool)

  • copy_input (bool)

  • pydeseq2_min_counts (int)

Return type:

tuple[AnnData, DataFrame, DataFrame]