LIANA+ provides an all-in-one framework for cell–cell communication inference
Daniel Dimitrov, Philipp Schäfer, Elias Farr, Pablo Rodríguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurélien Dugourd, Jovan Tanevski, Ricardo O. Ramirez Flores, Julio Sáez-Rodríguez
Abstract
The growing availability of single-cell and spatially resolved transcriptomics has led to the development of many approaches to infer cell-cell communication, each capturing only a partial view of the complex landscape of intercellular signalling. Here we present LIANA+, a scalable framework built around a rich knowledge base to decode coordinated inter- and intracellular signalling events from single- and multi-condition datasets in both single-cell and spatially resolved data. By extending and unifying established methodologies, LIANA+ provides a comprehensive set of synergistic components to study cell-cell communication via diverse molecular mediators, including those measured in multi-omics data. LIANA+ is accessible at https://github.com/saezlab/liana-py with extensive vignettes ( https://liana-py.readthedocs.io/ ) and provides an all-in-one solution to intercellular communication inference.