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>.