MMCCI: Multimodal Cell-Cell Interaction Integrative Analysis of Single Cell and Spatial Transcriptomics Data

Cell-cell interaction (CCI) analyses are an indispensable tool for harnessing the detail and depth of spatial and single-cell transcriptomics datasets by inferring inter-cellular communications, but no methods to integrate CCI results across samples exist currently. To address this, we have developed a computational pipeline, Multimodal CCI (MMCCI), to statistically integrate and analyze CCI results from existing popular CCI tools. We benchmarked MMCCI’s integration on single-cell spatial datasets and found it to be highly accurate compared to simpler methods. We utilized MMCCI’s integration and downstream biological analyses to uncover global and differential interaction patterns in multimodal aging brain and melanoma spatial datasets.