See cfRNA_pipeline folder for scripts used to processes sequencing data.
See Analysis_Scripts for code to reproduce all data analysis reported in main text and supplemental material, and generation of all figures.
R version 4.1 or higher. Python version 3.6 or higher. Snakemake version 6.5 or higher.
Processing pipeline recommended for use in a linux HPC environment.
No package installation is required, outside of R and python libraries referenced in codebase.
Run main_script.R in Analysis_Scripts folder to reproduce all experiment results. This should take less than 10 minutes on a typical computer. Expected output figures are included in Figures folder.