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correlation-methylation-epiFeatures

Integrate CpG methylation BED data with chromatin bigWig signals to generate region_signal_table.tsv and correlation matrices.

12|3|Updated Nov 4, 2025
Search Tags:#integration#correlation#chromatin#methylation#epigenomics#atac-seq
One-click install
npx skills add https://github.com/BIsnake2001/ChromSkills --skill correlation-methylation-epifeatures
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: correlation-methylation-epiFeatures
Source: https://github.com/BIsnake2001/ChromSkills/tree/main/27.correlation-methylation-epiFeatures
Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill correlation-methylation-epifeatures

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill enables researchers to integrate CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks to explore regulatory relationships and epigenomic coordination.

Core Features & Use Cases

  • Integrated region-level table: Aligns methylation with chromatin signals to build a unified region table for downstream analysis.
  • Correlation analysis: Computes pairwise correlations between methylation and chromatin features across genomic regions.
  • Visualization: Generates heatmaps and scatter plots to visualize methylation–signal associations.
  • Use Case: Compare promoter and enhancer regions across conditions to identify coordinated epigenetic changes.

Quick Start

Provide CpG methylation BED and bigWig chromatin tracks for your regions and run the pipeline to generate a region_signal_table and correlations.

Frequently Asked Questions about correlation-methylation-epiFeatures

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

FAQPage Schema
How do I integrate CpG methylation data with ATAC-seq and ChIP-seq chromatin signals?▼

To integrate CpG methylation with chromatin signals, provide methylation BED files and chromatin bigWig tracks to map region-level epigenetic relationships across regulatory regions like promoters and enhancers.

Can I calculate correlation between DNA methylation and histone marks like H3K27ac?▼

Yes, you can calculate correlation between DNA methylation and histone marks by processing methylation BED coverage and bigWig chromatin tracks to generate a feature correlation matrix.

What input file formats are required for methylation and chromatin signal correlation analysis?▼

Methylation and chromatin signal correlation analysis requires input BED files for CpG methylation coverage and bigWig files for chromatin features, along with optional target regions.

What outputs do I get from mapping methylation to chromatin features?▼

Mapping methylation to chromatin features outputs a region signal table TSV file containing aligned signals and a feature correlation matrix for downstream multi-omics analysis.

Does this methylation integration approach work for comparing promoter and enhancer regions across conditions?▼

Yes, this methylation integration approach works for comparing promoter and enhancer regions across conditions by aligning CpG methylation coverage with chromatin signals to identify coordinated epigenetic changes.

Are visualizations provided for exploring methylation and chromatin signal associations?▼

Yes, visualizations including heatmaps and scatter plots are generated to help researchers explore and interpret methylation and chromatin signal associations across analyzed genomic regions.

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