Dawnn benchmarking dataset: Simulated branching trajectories 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 simulated branching trajectories.

FILES:
Data processing code

adapted_traj_sim_milo_paper.R Lightly adapted code from Dann et al. to simulate single-cell RNAseq datasets that form branching trajectories .
generate_test_data_branching_traj_sim_milo_paper.R R code to assign simulated labels to datatsets generated from adapted_traj_sim_milo_paper.R. Seurat objects saved as cells_sim_branching_traj_gex_seed_*.rds. Simulated labels saved as benchmark_dataset_sim_branching_traj.csv.

Resulting datasets

cells_sim_branching_traj_gex_seed_*.rds Seurat objects generated by generate_test_data_branching_traj_sim_milo_paper.R.
benchmark_dataset_sim_branching_traj.csv Cell labels generated by generate_test_data_branching_traj_sim_milo_paper.R.

本项工程汇集了一系列文件，旨在使用户能够复现《Dawnn：基于神经网络的单细胞RNA测序数据集差异丰度检测》（Hall和Castellano，待审稿）中的模型开发与基准测试。Dawnn是一款旨在检测单细胞RNA测序数据集中差异丰度的工具，现已作为R语言包发布。如用户在复现本论文中任何分析时遇到困难，请与我方联系。本集合中的文件对应于基于模拟分支轨迹的基准测试数据集。

文件列表：
数据预处理代码
adapted_traj_sim_milo_paper.R：对Dann等人的代码进行轻微调整，以模拟形成分支轨迹的单细胞RNA测序数据集。
generate_test_data_branching_traj_sim_milo_paper.R：R语言代码，用于将模拟标签分配给由adapted_traj_sim_milo_paper.R生成的数据集。Seurat对象以cells_sim_branching_traj_gex_seed_*.rds保存。模拟标签以benchmark_dataset_sim_branching_traj.csv保存。
结果数据集
cells_sim_branching_traj_gex_seed_*.rds：由generate_test_data_branching_traj_sim_milo_paper.R生成的Seurat对象。
benchmark_dataset_sim_branching_traj.csv：由generate_test_data_branching_traj_sim_milo_paper.R生成的细胞标签。