Utility Functions
- utils.str_to_list(values)
Converting str representation of list to list
Parameters
values: str representation of list
Returns
values: list
- utils.prepare_markers(results, col_cluster, col_marker, output_folder='', outputfilename_prefix='')
Converting marker_genes_csv to dictionary (clusterName: marker_genes)
Parameters
- filename
csv with markers per cluster.
- col_cluster
Column name in file storing cell annotation.
- col_marker
Column name in file storing markers.
- output_folder
Output folder for missing genes.
- outputfilename_prefix
Prefix for missing genes file.
Returns
marker_genes_dict: dictionary (cluster: list of markers)
Creates files
{output_folder}{outputfilename_prefix}_not_found.csv: list of markers not found in anndata