README.md

Summary

Plots and analysis for Zhou et al., Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer, 2020.

Data used for these analyses can be found in data/. Analyses performed can be found in results/.

Setup

For reproducibility, the core packages (and their versions) used for these analyses can be found in environment.yaml. To reproduce this environment, use Conda with the following command:

conda env create --name Zhou2020 --file environment.yaml

This repository can be downloaded using git clone.

Analysis

To re-run the analysis in a specific folder (i.e. results/<analysis>/), simply run snakemake from within this folder, or follow the README.md files.