CellPhoneDB v2.0 is a comprehensive repository and computational framework for inferring cell-cell communication networks from single-cell transcriptomics data. The repository includes ligands, receptors, and their interactions, with a focus on the subunit architecture of both ligands and receptors to accurately represent heteromeric complexes. The framework uses statistical methods to predict enriched cellular interactions between two cell types based on the expression levels of ligands and receptors within each cell type. The protocol involves pre-processing raw data, generating input files, and running the analysis using either the interactive web portal or the Python package. The results include mean values, deconvoluted information, and p-values for significant interactions, which can be visualized using dot plots and heatmaps. The database and framework are publicly available at <https://github.com/Teichlab/cellphonedb> and <http://www.cellphonedb.org>, respectively. The authors demonstrate the utility of CellPhoneDB v2.0 through examples, including studies on maternal-fetal communication and tumor microenvironment dynamics.CellPhoneDB v2.0 is a comprehensive repository and computational framework for inferring cell-cell communication networks from single-cell transcriptomics data. The repository includes ligands, receptors, and their interactions, with a focus on the subunit architecture of both ligands and receptors to accurately represent heteromeric complexes. The framework uses statistical methods to predict enriched cellular interactions between two cell types based on the expression levels of ligands and receptors within each cell type. The protocol involves pre-processing raw data, generating input files, and running the analysis using either the interactive web portal or the Python package. The results include mean values, deconvoluted information, and p-values for significant interactions, which can be visualized using dot plots and heatmaps. The database and framework are publicly available at <https://github.com/Teichlab/cellphonedb> and <http://www.cellphonedb.org>, respectively. The authors demonstrate the utility of CellPhoneDB v2.0 through examples, including studies on maternal-fetal communication and tumor microenvironment dynamics.