# CyTOF analysis of periventricular immune cells in MS

# Purpose

The code in this repository was used to analyse the mass cytometry data of periventricular immune cells at postmortem septum, choroid plexus and blood from MS, dementia and neurological control donors. The results are presented in the manuscript "Single-cell profiling reveals periventricular CD56bright NK cell accumulation in multiple sclerosis". Additional details of the analysis are included in the method section of the manuscript.



# Population identification, differential abundance and marker expression
The files 'CP_CyTOF_analysis.R' and 'CP_CyTOF_analysis_zoom.R' contain the main scripts for analysing the general populations (Figures of the manuscript 1b-d, 4a-b, 6b-c) and zooming into subpopulations (Figures 2a and 2c, 3a-d, 5a-e, 7a-e), respectively. This includes clustering and analyses of differential abundance (DA) of cell populations and differential expression (DE) of markers. They call functions contained in the folder `custom-functions`.