This repository contains the complete data-processing pipeline used to generate all figures, analyses, and results for the manuscript Early Cancer Detection in Hereditary Breast and Ovarian Cancer Syndrome with Cell-Free DNA.
The pipeline runs end-to-end automatically: it prepares directories, checks and installs required packages, executes all analysis modules, and produces processed data tables, publication-ready figures, and HTML reports.
Please see the Data and Code Availability section in the Manuscript for the Zenodo link and download the raw_data input from Zenodo.
EarlyDetectionHBOC/
├── Install_Packages.R # Installs all required R packages
├── run_all_scripts.R # Master script that runs the entire pipeline
├── scripts/ # All analysis and figure-generation scripts
├── raw_data/ # Raw input data (downloaded from Zenodo if missing)
├── data/ # Intermediate processed data generated during runtime
├── figures/ # Final publication-ready figures generated by the pipeline.
├── HTML/ # Rendered HTML reports from RMarkdown files
└── README.md # Project documentation
- R: https://www.r-project.org
- RStudio (optional): https://posit.co/download/rstudio-desktop/
git clone https://github.com/pughlab/EarlyDetectionHBOC.git
cd EarlyDetectionHBOCDownload raw_data.zip from Zenodo (see link in Code and Data Availability), unzip it, and place the resulting raw_data/ directory in the project root.
Rscript Install_Packages.RThis script verifies and installs all necessary R package dependencies.
Rscript run_all_scripts.RDuring execution, the pipeline will automatically:
- generate processed datasets (
data/) - produce publication-ready figures (
figures/) - write rendered reports (
HTML/)
Author: Erik Ensminger - [email protected]