Dawnn benchmarking dataset: Simulated linear 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 linear 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 linear trajectories .
generate_test_data_linear_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_linear_traj_gex_seed_*.rds. Simulated labels saved as benchmark_dataset_sim_linear_traj.csv.

Resulting datasets

cells_sim_linear_traj_gex_seed_*.rds Seurat objects generated by generate_test_data_linear_traj_sim_milo_paper.R.
benchmark_dataset_sim_linear_traj.csv Cell labels generated by generate_test_data_linear_traj_sim_milo_paper.R.

本项研究汇集了一系列文件，旨在允许用户复现论文《Dawnn：基于神经网络的单细胞差异丰度检测》（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，现作为 R 软件包提供。若用户在复现论文中的任何分析时遇到困难，请与我们联系。本集合中的文件对应基于模拟线性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：从 Dann 等人（2017）的研究中轻量级改编的代码，用于模拟形成线性轨迹的单细胞 RNA 测序数据集。
generate_test_data_linear_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_linear_traj_gex_seed_*.rds 的形式保存，模拟标签以 benchmark_dataset_sim_linear_traj.csv 的形式保存。
结果数据集
cells_sim_linear_traj_gex_seed_*.rds：由 generate_test_data_linear_traj_sim_milo_paper.R 生成的 Seurat 对象。
benchmark_dataset_sim_linear_traj.csv：由 generate_test_data_linear_traj_sim_milo_paper.R 生成的细胞标签。