This release includes the first stable version of the methylation-pipeline, a modular Python-based framework for filtering, analyzing, and visualizing CpG methylation data across patient cohorts and treatment timepoints.
Key features:
🔧 Preprocessing tools to filter methylation matrices by patient ID
📊 Global and locus-level methylation summary statistics
🧬 Timepoint classification (Baseline, On-Treatment, Post-Treatment, Healthy)
🧼 Built-in visualization of methylation trajectories and distributions
📁 Outputs ready for downstream statistical or clustering analyses
This pipeline is intended for researchers working with EM-Seq or cfDNA methylation data and can be adapted to other bisulfite-free methylation sequencing datasets.
For full documentation and usage examples, please see the README.