czbenchmarks.datasets.utils_single_cell
=======================================

.. py:module:: czbenchmarks.datasets.utils_single_cell


Attributes
----------

.. autoapisummary::

   czbenchmarks.datasets.utils_single_cell.logger


Functions
---------

.. autoapisummary::

   czbenchmarks.datasets.utils_single_cell.run_multicondition_dge_analysis


Module Contents
---------------

.. py:data:: logger

.. py:function:: 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.

   :param adata (AnnData):
   :type adata (AnnData): Annotated data matrix containing gene expression and metadata.
   :param condition_key (str):
   :type condition_key (str): Column name for condition labels in `adata.obs`.
   :param de_gene_col (str):
   :type de_gene_col (str): Column name for gene labels in `adata.var`.
   :param control_cells_ids (Dict[str:
   :type control_cells_ids (Dict[str: Mapping from condition -> list of matched control cell ids.
   :param List[str]]):
   :type List[str]]): Mapping from condition -> list of matched control cell ids.
   :param filter_min_cells (int:
   :type filter_min_cells (int: Minimum number of cells expressing a gene to include that gene. Defaults to 10.
   :param optional):
   :type optional): Minimum number of cells expressing a gene to include that gene. Defaults to 10.
   :param filter_min_genes (int:
   :type filter_min_genes (int: Minimum number of genes detected per cell. Defaults to 1000.
   :param optional):
   :type optional): Minimum number of genes detected per cell. Defaults to 1000.
   :param min_pert_cells (int:
   :type min_pert_cells (int: Minimum number of perturbed cells required. Defaults to 50.
   :param optional):
   :type optional): Minimum number of perturbed cells required. Defaults to 50.
   :param remove_avg_zeros (bool:
   :type remove_avg_zeros (bool: Whether to remove genes with zero average expression. Defaults to True.
   :param optional):
   :type optional): Whether to remove genes with zero average expression. Defaults to True.
   :param store_dge_metadata (bool:
   :type store_dge_metadata (bool: Whether to store DGE metadata in the results DataFrame. Defaults to False.
   :param optional):
   :type optional): Whether to store DGE metadata in the results DataFrame. Defaults to False.
   :param return_merged_adata (bool:
   :type return_merged_adata (bool: Whether to return the merged AnnData object. Defaults to False.
   :param optional):
   :type optional): Whether to return the merged AnnData object. Defaults to False.

   :returns: (results_df, adata_merged):
             - results_df: Differential expression results for `selected_condition`.
             - adata_merged: AnnData containing concatenated condition and control cells.
   :rtype: Tuple[pd.DataFrame, anndata.AnnData]