VisiumMS

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

This pipeline uses Snakemake to ensure reproducibility

Data

Processed data in h5ad format can be downloaded from the Human Cell Atlas portal, while raw data is available on GEO.

Installation

Clone repo:

git clone git@github.com:saezlab/VisiumMS.git
cd VisiumMS

Install mamba (this might take a while) to install packages faster:

conda install -n base -c conda-forge mamba

Then create a new enviroment specific for Snakemake:

mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

To run specific outputs you can run:

snakemake --profile config/slurm/  path/to/output/file 

To run the complete processing of the data (this can take a while), run:

snakemake --profile config/slurm/

Reference

Lerma-Martin, C., Badia-i-Mompel, P., Ramirez Flores, R.O. et al. Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions. Nat Neurosci 27, 2354–2365 (2024). https://doi.org/10.1038/s41593-024-01796-z