Evaluation of (Semi-)Automated Gating Tools on FACS Data

Team Members:
Timo, Leo, Mahima, Rebecca, Lisa

Supervisors:
Lis, Judith, Quirin

Overview

This project evaluates (semi-)automated gating tools for Flow Cytometry Analysis (FACS) data. The comparison is done using several metrics and visualizations (chord plots and heatmaps). The tools' performance is analyzed and compared across multiple metrics to manual gating and each other.

Directory Structure

• tool_code/: Each tool has its own folder containing the code used to run it, along with any adjustments made during the process.
• metrics_all_against_all_based_on_results_folder/: Contains the script and the start script for calculating metrics when comparing all tools against all.
• chord_plots_based_on_results_folder/: Scripts for generating chord plots based on the results.
• create_heatmaps/: Script for generating heatmaps.
• results_celltypes/: The final predictions for each tool are available in this .zip file.
• classification_matrix.csv: The final classification matrix used for this analysis.
• mapping_cell_types_labels.csv: The final mapping file for the cell types needed in some scripts.
• renv/: Each subfolder containing R code has its own environment managed by renv.
• plots/: Final plots generated by the code are added as subfolders containing the plots.
• archive/: Contains older scripts that are no longer used or code that has been adjusted.