Here you can find the datasets used for development, validation and application of NicheNet, a method that links ligands to target genes to model intercellular communictation. The software to use NicheNet (i.e. R package nichenetr) is available at: https://github.com/saeyslab/nichenetr Short description of individual files: * data for development of NicheNet: - lr_network.rds: network containing ligand-receptor interactions - signaling_network.rds: network containing signaling interactions - gr_network.rds: network containing gene regulatory interactions - weighted networks.rds: integrated weighted ligand-signaling and gene regulatory network * data for use of NicheNet: - ligand_tf_matrix.rds: matrix containing ligand-gene signaling scores - tf_target_matrix.rds: matrix containing gene-gene regulatory scores - ligand_target_matrix.rds: matrix containing ligand-target gene regulatory potential scores * datasets for validation of NicheNet: - expression_settings.rds: 111 expression datasets profiling the transcriptional response to a ligand * datasets to demonstrate application possibilities of NicheNet: - pemt_signature.txt: p-EMT geneset for which upstream regulators will be predicted - hnscc_expression.rds: single-cell expression data of malignant and non-malignant cells from head and neck squamous cell carcinoma tumors