This is a repository of the code and resources necessary to run the downstream analysis described in the paper cell atlas of the human omentum in health and metastasis reveals mechanisms of tissue homeostasis and reprogramming in response to ovarian cancer colonization by Lischetti et al.
The repository has the following structure:
- docs: additional readme documents for procedures. Code includes inline comments, but additional details can be found in this folder
- omentum_required: resources and configuration file either mandatory for scripts to run successfully or necessary to replicate the final results
- scripts: collection of scripts used for the downstream analysis and visualization. Each sub-directory includes scripts for a specific analysis type
- snake_files: custom configuration used for the snakemake pipeline