Ocrevus_manuscript

This repository contains the code associated with the manuscript Transcriptomic profiling after B-cell depletion reveals central and peripheral immune cell changes in multiple sclerosis. Analyzed Seurat objects are available on figshare

Disclaimer

• Throughout this project, We use the SLURM job scheduling system to run some of the "heavy" analyses on the Yale University HPC clusters.
• The code and additional resources on figshare.com are provided as-is. We have validated that this runs without errors on the HPC cluster and on local MacOS systems, but do not guarantee that this will be the case in different computing environments.
• Main analyses portion of this code are written with relative paths that have as root project this directory, but some path might need to be adjusted for the T cell analysis.

Content

• master.R details all procedures run throughout the project to generate the findings presented in the manuscript. It calls scripts stored in src and doc and is used to document the analysis steps.
• src contains all analyses steps
• doc contains Rmd documents used for data exploration and visualization.
• prepare_final_objects.R details the procedure to generate the objects uploaded on figshare.