Development, evaluation and application of NicheNet: datasets
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. 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
Files
pemt_signature.txt
Files
(382.6 MB)
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