Dawnn benchmarking dataset: Organoid processing and label simulation

This project is a collection of files to allow users to reproduce the model development and benchmarking in "Dawnn: single-cell differential abundance with neural networks" (Hall and Castellano, under review). Dawnn is a tool for detecting differential abundance in single-cell RNAseq datasets. It is available as an R package here. Please contact us if you are unable to reproduce any of the analysis in our paper. The files in this collection correspond to the benchmarking dataset based on single-cell RNAseq of bile duct organoids. <br> FILES: Input datasets Dataset from "Cholangiocyte organoids can repair bile ducts after transplantation in the human liver". Science 371(6531) pp. 839-846 (2021). <strong>E-MTAB-8495.aggregated_filtered_normalised_counts.mtx</strong> Single-cell RNAseq expresison matrix. <strong>E-MTAB-8495.aggregated_filtered_normalised_counts.mtx_cols</strong> Column names. <strong>E-MTAB-8495.aggregated_filtered_normalised_counts.mtx_rows</strong> Row names. Data processing code <strong>process_organoid_cells_data.R</strong> Generates benchmarking dataset from input data. (Reads <em>E-MTAB-8495.aggregated_filtered_normalised_counts.*</em> files; Runs the standard Seurat pipeline; Saves the resulting Seurat dataset as<em> organoid_cells.RDS</em>) <strong>simulate_organoid_labels_Rscript.R</strong> R code to simulate labels for benchmarking. <strong>simulate_organoid_labels_bash.sh </strong>Bash script to execute <em>simulate_organoid_labels_Rscript.R</em>. Outputs stored in <em>benchmark_dataset_organoid_labels.csv</em>. Resulting datasets <strong>organoid_cells.RDS</strong> Seurat dataset generated by <em>process_organoid_cells_data.R</em>. <strong>benchmark_dataset_organoid_labels.csv </strong>Cell labels generated by <em>simulate_organoid_labels_bash.sh</em>.

本项目汇集了一系列文件，供用户复现《Dawnn：基于神经网络的单细胞差异丰度分析》（Hall与Castellano，审稿中）一文所述的模型开发与基准测试过程。Dawnn是一款用于检测单细胞RNA测序（single-cell RNAseq）数据集差异丰度的工具，已以R包形式在此处提供。若您无法复现论文中的任何分析内容，请与我们联系。本集合中的文件对应于基于胆管类器官单细胞RNA测序的基准测试数据集。<br> FILES: 输入数据集 来自《胆管细胞类器官可在人肝移植后修复胆管》一文的数据集（Science, 2021, 371(6531): 839-846）。<strong>E-MTAB-8495.aggregated_filtered_normalised_counts.mtx</strong> 单细胞RNA测序表达矩阵。<strong>E-MTAB-8495.aggregated_filtered_normalised_counts.mtx_cols</strong> 列名。<strong>E-MTAB-8495.aggregated_filtered_normalised_counts.mtx_rows</strong> 行名。数据处理代码 <strong>process_organoid_cells_data.R</strong> 从输入数据生成基准测试数据集（读取<em>E-MTAB-8495.aggregated_filtered_normalised_counts.*</em>文件；运行标准Seurat流程；将生成的Seurat数据集保存为<em>organoid_cells.RDS</em>）。<strong>simulate_organoid_labels_Rscript.R</strong> 用于模拟基准测试标签的R代码。<strong>simulate_organoid_labels_bash.sh</strong> 执行<em>simulate_organoid_labels_Rscript.R</em>的Bash脚本，输出结果存储于<em>benchmark_dataset_organoid_labels.csv</em>。生成的数据集 <strong>organoid_cells.RDS</strong> 由<em>process_organoid_cells_data.R</em>生成的Seurat数据集。<strong>benchmark_dataset_organoid_labels.csv</strong> 由<em>simulate_organoid_labels_bash.sh</em>生成的细胞标签。