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 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本数据集包含用于开发、验证及应用NicheNet的相关数据，NicheNet是一种可将配体与靶基因关联以构建细胞间通信模型的方法。NicheNet的使用软件（即R包nichenetr）可从以下地址获取：https://github.com/saeyslab/nichenetr 各文件简要说明： - NicheNet开发所用数据： - lr_network.rds：包含配体-受体相互作用的网络文件 - signaling_network.rds：包含信号传导相互作用的网络文件 - gr_network.rds：包含基因调控相互作用的网络文件 - weighted_networks.rds：整合了配体信号传导与基因调控的加权网络文件 - NicheNet使用所需数据： - ligand_tf_matrix.rds：包含配体-基因信号传导评分的矩阵文件 - tf_target_matrix.rds：包含基因-基因调控评分的矩阵文件 - ligand_target_matrix.rds：包含配体-靶基因调控潜能评分的矩阵文件 - NicheNet验证所用数据集： - expression_settings.rds：共111个表达数据集，用于分析配体处理后细胞的转录响应 - 用于演示NicheNet应用场景的数据集： - pemt_signature.txt：p-EMT基因集，用于预测其上游调控因子 - hnscc_expression.rds：头颈部鳞状细胞癌肿瘤中恶性与非恶性细胞的单细胞表达数据