Welcome to DiffMethylTools

DiffMethylTools is a comprehensive, command-line suite for DNA methylation analysis. It is designed to take you from raw alignment data to rich genomic annotations and publication-ready visualizations in minutes.

DiffMethylTools Workflow

Why DiffMethylTools?

Flexible Input: Supports both BED and Bismark Cytosine Report (CR) formats natively, with options for fully custom column mapping.
Fast & Automated: Run full pipelines from DMR (Differentially Methylated Regions) generation to annotation with a single command.
Rich Visualizations: Automatically generate Volcano plots, Manhattan plots, region annotations, and methylation curves.

Sample Plot1 Sample Plot2

Ready to begin? Head over to the Installation page to get set up!