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: 

- 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: >50 expression datasets profiling the transcriptional response to a ligand

* datasets to demonstrate application possibilities of NicheNet:

- 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