The score is the average expression of a set of genes subtracted with the average expression of a reference set of genes. The reference set is randomly sampled from the gene_pool for each binned expression value.
This reproduces the approach in Seurat [Satija15] and has been implemented for Scanpy by Davide Cittaro.
The list of gene names used for score calculation.
Number of reference genes to be sampled. If len(gene_list) is not too low, you can set ctrl_size=len(gene_list).
Genes for sampling the reference set. Default is all genes.
Number of expression level bins for sampling.
Name of the field to be added in .obs.
The random seed for sampling.
Depending on copy, returns or updates adata with an additional field score_name.