cfMeDIP-seq Manuscript Repository

This repository contains all major analysis scripts and code for generating figures presented in our cfMeDIP-seq manuscript. The materials provided here support the reproducibility and transparency of our research findings.

Overview

Cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) is a powerful approach for analyzing DNA methylation patterns in cell-free DNA. This repository accompanies our manuscript and provides the computational framework used for data analysis and visualization.

Repository Contents

• Scripts: Core scripts for processing cfMeDIP-seq data, including quality control, transforming raw sequencing data into analysis-ready formats, and differential methylation analysis
• Figures: Code to reproduce all main model figures and supplementary figures from the manuscript
• Model Scripts Scripts for building and validating predictive models based on methylation signatures

Requirements

The analysis pipeline requires the following:

• R (version 4.0 or higher)

Citation

If you use code or methods from this repository, please cite our manuscript:

TBA

Contact

For questions or issues related to this repository, please contact:

Robert Kridel - Robert.Kridel@uhn.ca