Dawnn benchmarking dataset: Mouse embryo cells 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 mouse emrbyo cells. <br> FILES: Input data Dataset from: "A single-cell molecular map of mouse gastrulation and early organogenesis". Nature 566, pp490–495 (2019). The input data is loaded from the <em>MouseGastrulationData</em> R package. We upload here the RDS file generated by loading the dataset in <em>process_mouse_cells.R</em> in case the R package becomes unavailable <strong>MouseGastrulationData_loaded_dataset.RDS</strong> Dataset loaded from <em>MouseGastrulationData</em> R package in <em>process_mouse_cells.R</em> (in call to <em>EmbryoAtlasData</em> function). Data processing code <strong>process_mouse_cells.R</strong> Generates benchmarking dataset from input data. (Loads input data; Runs the standard single-cell RNAseq pipeline). Follows Dann <em>et al.</em> Resulting dataset saved as <em>mouse_gastrulation_data_regen.RDS</em>. <strong>simulate_mouse_pc1_Rscript.R</strong> R code to simulate <em>P(Condition_1</em>)s for benchmarking. <strong>simulate_mouse_pc1_bash.sh </strong>Bash script to execute <em>simulate_mouse_pc1_Rscript.R</em>. Outputs stored in <em>benchmark_dataset_mouse_pc1s_regen.csv</em>. <strong>simulate_mouse_labels_Rscript.R</strong> R code to simulate labels for benchmarking. <strong>simulate_mouse_labels_bash.sh </strong>Bash script to execute <em>simulate_mouse_labels_Rscript.R</em>. Outputs stored in <em>benchmark_dataset_mouse.csv</em>. Resulting datasets <strong>mouse_gastrulation_data_regen.RDS</strong> Seurat dataset generated by <em>process_mouse_cells.R</em>. <strong>benchmark_dataset_mouse.csv </strong>Cell labels generated by<em> simulate_mouse_labels_bash.sh.</em> <strong>benchmark_dataset_mouse_pc1s_regen.csv</strong> <em>P(Condition_1</em>)s generated by<em> simulate_mouse_pc1_bash.sh.</em>