CSF Immune Atlas Code

This repository contains the code used in the manuscript Atlas of cerebrospinal fluid immune cells across neurological diseases published in Annals of Neurology 2024.

Structure

Directory	Description
scripts/analysis	Code used for the analysis in the manuscript
models	Final XGB models

Package for helper functions

Helper functions of this analysis are bundled in the package CSFAtlasTools

Reproducibility

To ensure reproducibility, we used the renv package and Docker. To restore the packages from the renv.lock file, use:

renv::restore()

Alternatively, you can also use the Docker image, which contain all necessary R packages and system dependencies. The Docker image is available on DockerHub:

docker pull mihem/csf_immune_atlas:2.0

Contact

If you have any questions, please contact me via mheming.com.