crested.tl.modisco.calculate_mean_expression_per_cell_type

crested.tl.modisco.calculate_mean_expression_per_cell_type(file_path, cell_type_column, cpm_normalize=False)

Read an AnnData object from an H5AD file and calculates the mean gene expression per cell type subclass.

Parameters:

• file_path (str) – The path to the H5AD file containing the single-cell RNA-seq data.

• cell_type_column (str) – The column name in the cell metadata that defines the cell type subclass.

• cpm_normalize (bool (default: False)) – Whether to additionally cpm_normalize the scRNA-seq data.

Return type:

DataFrame

Returns:

A DataFrame containing the mean gene expression per cell type subclass.