Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GRNs. See more details at Zhang, S., Pyne, S., Pietrzak, S. et al. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun 14, 3064 (2023). https://doi.org/10.1038/s41467-023-38637-9 The source data scMTNI_sourcedata.tar.gz contains the following 3 parts: 1) The cluster-specific scRNA-seq matrices and the prior networks for all three datasets and scMTNI inferred consensus networks. 2) Gold standard human and mouse datasets for evaluation. 3) Source data for scMTNI figures 2-8 and supplementary figures. The key for each figure and its corresponding file path is in SourceData_Key_v2.xlsx. The source data Buenrostro_Hematopoiesis.tar.gz contains the scRNA-seq data for human hematopoietic differentiation downloaded from Data S2 of Buenrostro et al. The source data RawMotifFiles.tar.gz contains the motif instance files and promoter files for human and mouse for generating prior networks using scATAC-seq data for scMTNI. Check https://github.com/Roy-lab/scMTNI/blob/master/Scripts/genPriorNetwork/readme.md for examples and scripts. The Buenrostro_priorNetwork_bamfiles.tar.gz contains the raw bam files of scATAC-seq data for human hematopoietic differentiation downloaded from Buenrostro et al.本次上传的文件为scMTNI算法的源数据集。scMTNI是一种多任务学习框架，可整合细胞谱系结构、scRNA-seq（单细胞RNA测序）与scATAC-seq（单细胞染色质转座酶可及性测序）数据，实现细胞类型特异性基因调控网络（GRNs，Gene Regulatory Networks）的联合推断。详细信息可参阅文献：Zhang S, Pyne S, Pietrzak S 等. 基于单细胞多组学数据集的细胞谱系上的细胞类型特异性基因调控网络推断. 自然-通讯, 2023, 14:3064. DOI: 10.1038/s41467-023-38637-9 源数据集scMTNI_sourcedata.tar.gz包含以下3个部分： 1. 所有三个数据集的聚类特异性scRNA-seq矩阵、先验网络，以及scMTNI推断得到的一致性网络。 2. 用于评估的金标准人类与小鼠数据集。 3. scMTNI论文图2至图8及补充图的源数据。各图对应的标注文件与路径信息已收录于SourceData_Key_v2.xlsx中。 源数据集Buenrostro_Hematopoiesis.tar.gz包含从Buenrostro等文献的补充材料S2中获取的人类造血分化过程的scRNA-seq数据。 源数据集RawMotifFiles.tar.gz包含用于scMTNI借助scATAC-seq数据构建先验网络的人类与小鼠的基序实例文件及启动子文件。相关示例代码与脚本可参阅：https://github.com/Roy-lab/scMTNI/blob/master/Scripts/genPriorNetwork/readme.md 源数据集Buenrostro_priorNetwork_bamfiles.tar.gz包含从Buenrostro等文献获取的人类造血分化过程scATAC-seq数据的原始bam文件。