Datasets for the intercellular communication analysis of Hi-C3

scRNA-seq data from 4 cases (with 63689, 43817, 11167, and 12307 cells, respectively) of colorectal cancer were available from the Gene Expression Omnibus (GEO) database under accession code GSE132465, GSE146771, and GSE236581.scRNA-seq datasets from four Arabidopsis thaliana samples (containing 5826, 6658, 5042, and 5186 cells, respectively), used for evaluating pairwise communication inference performance, were obtained from the GEO database under accession codes GSE123818, GSE158761, GSE161482, and GSE161332. In addition, four single-cell–resolution spatial transcriptomics datasets from Arabidopsis thaliana leaf tissues were obtained from the Spatial Transcript Omics Database (STOmics DB) under accession number STDS0000104. For the colorectal cancer case, we used the CellChatDB, which is widely recognized for its extensive collection of human ligand-receptor pairs. CellChatDB includes a total of 3249 ligand-receptor pairs. For the Arabidopsis thaliana cases, we used PlantPhoneDB, which contains 3514 ligand-receptor pairs relevant to plant cell signaling pathways.