This directory contains scripts used to analyze and visualize data for Van Deusen, et al. 

01_Data_Preprocessing: Scripts to pre-process mass cytometry data for quality control

02_UMAP_and_Leiden_Clustering: Scripts for dimensionality reduction and clustering analyses

03_Protein_RNA_Comparison: Scripts for comparison of mass cytometry with scRNA-seq and in situ 
hybridization data from the Allen Institute Developing Mouse Brain Atlas

04_URD: Scripts to perform pseudotime-based trajectory analyses of mass cytometry data with URD

05_Figure_Outputs: Scripts used to generate visual outputs presented in figures. 

Please note that figure panels without designated scripts were generated using Adobe Illustrator and BioRender (https://biorender.com), or were automated outputs of the URD R package (Extended Data Figures 7a-d, 8g-j).