The workflow of DeCEP. (A) DeCEP leverages pre-existing functional gene lists from various databases as prior knowledge to construct static or dynamic functional networks using directed graphs that are tailored to specific cellular contexts in single-cell RNA sequencing (scRNA-seq) data. Based on the topology of these functional networks, DeCEP identifies context-dependent hub genes, calculates DeCEP scores, and determines the states of individual cells. (B) DeCEP anchors cell states to spatial locations in spatial transcriptomics (ST) data. DeCEP constructs functional networks tailored to spatial contexts, focusing on regions of interest (ROIs) and their corresponding neighborhoods. DeCEP then identifies spatially dependent hub genes and assigns DeCEP scores.