This repository contains the analysis scripts used in the study: "Multimodal plasma and urinary cell-free DNA profiling improves risk stratification in newly diagnosed prostate cancer"
The custom analysis scripts were developed for the genomic and epigenomic analyses of plasma and urinary cell-free DNA (cfDNA) from prostate cancer patients and cancer-free controls:
Genomic analyses:
- Copy number variation (CNV) analysis
- Chromosomal instability analysis (CIA)
Epigenomic analyses:
- cfDNA fragmentation analysis
- Methylation profiling
The provided scripts cover data preprocessing, quality control, statistical analysis, and visualization relevant to each analysis type. Established computational algorithms and previously published tools were adapted and extended for study-specific purposes.
The code is provided in its current implementation and may need to be adapted for compatibility with other datasets or study designs.
Data availability Due to privacy and ethical considerations, raw input data (e.g., sequencing files) are not included in this repository.
For questions or additional information, please reach out to: Dr. Anja Lisa Riediger (a.riediger@dkfz-heidelberg.de)