schae211 / VisiumMS_copy

VisiumMS

Scripts to reproduce results from "Spatial cell type mapping of multiple sclerosis lesions".

Structure

Inside scripts there are different subdirectories:

• figures/: Python and R scripts to reproduce the mansucript's figures
• launchers/: Scripts to send jobs to the cluster using SLURM
• pipeline/: Scripts to run processing scripts in process sequentaly
• plot/: General plotting scripts
• process/: Scripts to process the raw snRNA-seq and Visium data
• smFISH/: Scripts to reproduce the smFISH imaging quantification

Reference

Lerma-Martin, C., Badia-i-Mompel, P. et al. Spatial cell type mapping of multiple sclerosis lesions. bioRxiv 2022.11.03.514906 (2022) doi:10.1101/2022.11.03.514906.