Data For Development, Evaluation And Application Of Nichenet

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/browaeysrobin/nichenetr Short description of individual files: * data for development of NicheNet ("networks" subdirectory) - 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 ("model" subdirectory): - 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 ("validation" subdirectory): - expression_settings.rds: >50 expression datasets profiling the transcriptional response to a ligand * datasets to demonstrate application possibilities of NicheNet ("application" subdirectory) - gene_signature_pemt.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