/VisiumMS

Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

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.