Development, evaluation and application of NicheNet: datasets

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

The ligand-target matrix of this Zenodo repository version specifically was used for the NicheNet analyses as described in the paper "Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche" from Bonnardel, T'jonck et al. (https://www.cell.com/immunity/fulltext/S1074-7613(19)30368-1.) 

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:

- 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