Here the user can find the organization of the whole package:

• single_cell_processing - all scripts, pipelines and modules that process single-cell datasets, containing mostly analysis that is done prior to network inference
• network_inference - all scripts, pipelines and modules that are required for gene regulatory network inference (GRN) based on pySCENIC (Van de Sande et al., 2020) package
• network_analysis - analysis of computed GRNs, includes exploration of network structure, community analysis and gene set enrichment analysis (GSEA)