cfMIND: A read-level methylation framework for accurate non-invasive disease detection using cell-free DNA

1.scripts This repository contains analysis scripts used to generate results for the cfMIND manuscript, including multi-assay cfDNA methylation data preprocessing, benchmarking of comparator methods, evaluation of cfMIND performance, and biological characterization of disease-associated features (ALS and COAD). For detailed documentation, function descriptions, and execution guidelines, please see the README.md file. 2.cfMIND Example Data This repository contains example files for cfMIND (cfDNA Methylation signals of INdividual read for disease Detection), a machine learning-based framework for sensitive and robust disease detection using cfDNA methylation signals at the individual read level. These files are provided to help users test the environment setup and quickly get started with cfMIND, including both feature extraction and disease detection steps. Example input files for cfMIND: (1)Bams/ *.bam – Sorted BAM files *.bam.bai – BAM index files (2)CpGs/ CpG_OB*.txt – CpG methylation calls (original bottom strand) CpG_OT*.txt– CpG methylation calls (original top strand) (3)manifest.txt – Contains the file paths to all BAM files and their corresponding CpG files, along with sample labels.