Introduction

The CCI (Cell-Cell Interaction) module is used for cell communication analysis of spatial transcriptomics and single-cell data. It supports two algorithms: cellchat and cellphonedb, and outputs results such as interaction strength, pathways, and networks.

Reference

• Jin, S., Plikus, M. V., & Nie, Q. (2025). CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics. Nature protocols, 20(1), 180-219.

• Troulé, K., Petryszak, R., Cakir, B., Cranley, J., Harasty, A., Prete, M., ... & Vento-Tormo, R. (2025). CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data. Nature Protocols, 1-29.