pyXenium.cci

cci_topology_analysis

Score cell-cell interaction hypotheses using topology anchors, sender/receiver expression support, and de-saturated local contact structure.

Publication-facing optional outputs

cci_topology_analysis keeps the original discovery score as the default behavior. For manuscript-grade analyses, the function can also annotate interaction modes, apply mechanism-aware distance kernels, compute a lightweight component-shuffle null calibration (cci_pvalue, cci_fdr, null_z), attach receiver downstream-response support, and return the top-axis hotspot table.

These additions are designed as computational evidence layers. They prioritize cell-cell interaction hypotheses but do not prove protein binding, secretion, or causal signaling.