ICELLNET v2: a versatile method for cell–cell communication analysis from human transcriptomic data

Abstract

Abstract Summary Several methods have been developed in the past years to infer cell–cell communication networks from transcriptomic data based on ligand and receptor expression. Among them, ICELLNET is one of the few approaches to consider the multiple subunits of ligands and receptors complexes to infer and quantify cell communication. In here, we present a major update of ICELLNET. As compared to its original implementation, we (i) drastically expanded the ICELLNET ligand-receptor database from 380 to 1669 biologically curated interactions, (ii) integrated important families of communication molecules involved in immune crosstalk, cell adhesion, and Wnt pathway, (iii) optimized ICELLNET framework for single-cell RNA sequencing data analyses, (iv) provided new visualizations of cell–cell communication results to facilitate prioritization and biological interpretation. This update will broaden the use of ICELLNET by the scientific community in different biological fields. Availability and implementation ICELLNET package is implemented in R. Source code, documentation and tutorials are available on GitHub (https://github.com/soumelis-lab/ICELLNET).