https://github.com/saezlab/visiumms
Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.
https://github.com/saezlab/visiumms
Last synced: over 1 year ago
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Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.
- Host: GitHub
- URL: https://github.com/saezlab/visiumms
- Owner: saezlab
- License: gpl-3.0
- Created: 2021-09-07T19:02:54.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2024-12-11T21:18:59.000Z (over 1 year ago)
- Last Synced: 2025-03-28T05:51:06.321Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 42.5 MB
- Stars: 7
- Watchers: 2
- Forks: 5
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](https://explore.data.humancellatlas.org/projects/4c8e9d75-d85a-47de-9598-06549cf44b91), while raw data is available on [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279183).
## 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