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methylation-analysis

Analyze DNA methylation data with alignment, DMR analysis, and QC.

25|5|Updated Mar 22, 2026
Search Tags:#sequencing#qc#methylation#epigenomics#dmr#bisulfite
One-click install
npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill methylation-analysis-zongtingwei
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: methylation-analysis
Source: https://github.com/zongtingwei/Bioclaw_Skills_Hub/tree/main/skills/epigenomics-and-regulation/methylation-analysis
Command: npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill methylation-analysis-zongtingwei

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Automates and standardizes DNA methylation analyses, from alignment or methylation calling to DMR analysis, methylation QC, and locus-level interpretation, enabling reproducible epigenomics workflows.

Core Features & Use Cases

  • End-to-end methylation analysis: alignment/calling, DMR analysis, QC, and locus interpretation.
  • Versatile data support: works with bisulfite and long-read methylation data; outputs methylation calls, DMR tables, and QC plots.
  • Tooling and visualization: uses Bismark-like workflows; Python (pandas, matplotlib, seaborn) for summarization and visualization.
  • Real-world use case: identify differential methylation between conditions and annotate to promoters across samples.

Quick Start

Provide methylation-aware reads, a reference genome, and sample metadata to start the methylation analysis workflow.

Frequently Asked Questions about methylation-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run end-to-end DNA methylation analysis from reads to DMR interpretation?▼

DNA methylation analysis automates the full workflow from aligning methylation-aware reads and calling methylation to performing DMR analysis, QC, and locus-level interpretation for epigenomics studies.

What is the best way to identify differential methylation between conditions using bisulfite data?▼

Bisulfite methylation data can be processed using Bismark-like workflows to call methylation, perform DMR analysis between conditions, and annotate regions to promoters across samples.

Does this methylation analysis workflow support long-read sequencing data?▼

Methylation analysis supports both bisulfite and long-read methylation data, enabling locus- and region-level summaries and QC artifacts to support downstream interpretation.

Do I need a specific reference genome build to perform methylation QC and DMR analysis?▼

Methylation QC and DMR analysis require clear genome builds and version tracking to ensure reproducible results when aligning methylation-aware reads.

Can I use Python tooling like pandas and seaborn to visualize methylation QC artifacts?▼

Methylation QC artifacts and visualizations are generated using Python-based tooling including pandas for summarization and matplotlib with seaborn for plotting.

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