Cell Distance Analysis for Spatial Omics Datasets

Cell Distance Analysis for Spatial Omics Datasets, primarily focused on vascular cells.

The notebooks are designed to process and analyze the distances between cells in spatial omics datasets, with a particular focus on endothelial cells. They calculate the distances between all pairs of cells and visualize the distribution of these distances. The notebooks also include functionality to filter the data based on specific cell types and to visualize the results using histograms, violin plots, and other visualizations.

For Developers

The repository uses quarto for documentation and nbdev for notebook processing.

To update the README file from the nbs/index.ipynb notebook, run the following command in the root directory of the repository:

nbdev_readme

Then, to save the notebooks and render them using the nbdev library, you can run the following command in the root directory of the repository:

rm -rf _proc && nbdev_proc_nbs && cd _proc && quarto publish gh-pages --no-prompt

Then, push to GitHub:

git add .
git commit -m 'Updated repo' # Update this text with your own message
git push

The rendered and deployed notebooks will be available via GitHub Pages at the following URL:

https://cns-iu.github.io/hra-cell-distance-analysis