R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

NicheNet: predict active ligand-target links between interacting cells

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

LIANA: a LIgand-receptor ANalysis frAmework

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

A manually curated database of literature-supported ligand-receptor interactions in human and mouse

Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods

Entrain: Predicting Environmental Regulators of Differentiation Trajectories

Source code for Liu, Y., Li, J. S. S., Rodiger, J., Comjean, A., Attrill, H., Antonazzo, G., ... & Perrimon, N. (2022). FlyPhoneDB: an integrated web-based resource for cell–cell communication prediction in Drosophila. Genetics, 220(3), iyab235.

Infer cell-cell communications based on feed-forward neural network

This repo accompanies the Soelter et al., 2024 manuscript "Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq"

Investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data

Differential communication analysis for scRNAseq datasets based on expression products

SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

scMLnet2.0: Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks