czbenchmarks.datasets.utils_single_cell

Attributes

logger

Functions

run_multicondition_dge_analysis(...)

Run differential gene expression analysis for a list of conditions between perturbed

Module Contents

czbenchmarks.datasets.utils_single_cell.logger

czbenchmarks.datasets.utils_single_cell.run_multicondition_dge_analysis(adata: anndata.AnnData, condition_key: str, de_gene_col: str, control_cells_ids: Dict[str, List[str]], filter_min_cells: int = 10, filter_min_genes: int = 1000, min_pert_cells: int = 50, remove_avg_zeros: bool = False, store_dge_metadata: bool = False, return_merged_adata: bool = False) → Tuple[pandas.DataFrame, anndata.AnnData]

Run differential gene expression analysis for a list of conditions between perturbed

and matched control cells.

Parameters:

• (AnnData) (adata)

• (str) (de_gene_col)

• (str)

• (Dict[str (control_cells_ids)

• List[str]]) (Mapping from condition -> list of matched control cell ids.)

• (int (min_pert_cells)

• optional) (Whether to return the merged AnnData object. Defaults to False.)

• (int

• optional)

• (int

• optional)

• (bool (return_merged_adata)

• optional)

• (bool

• optional)

• (bool

• optional)

Returns:

(results_df, adata_merged): - results_df: Differential expression results for selected_condition. - adata_merged: AnnData containing concatenated condition and control cells.

Return type:

Tuple[pd.DataFrame, anndata.AnnData]