Data for development, evaluation and application of NicheNet

DOI10.5281/zenodo.1484084Zenodo1484084MaRDI QIDQ6690044FDOQ6690044

Dataset published at Zenodo repository.

Yvan Saeys, Robin Browaeys, Wouter Saelens

Publication date: 12 November 2018

Description

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.Thesoftware to use NicheNet (i.e. R package nichenetr) is available at: https://github.com/browaeysrobin/nichenetr Short description of individual files: * datafor 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-genesignaling 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 validationof 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

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