correlation-methylation-epiFeatures
This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks/TF signals.
npx skills add majiayu000/claude-skill-registry --skill 27-correlation-methylation-epifeatures --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Integrative Analysis of DNA Methylation and Chromatin Features ## 1. Overview Main steps include: - Refer to the **Inputs & Outputs** section to check required inputs and set up the output directory structure. - **Always prompt user** for genome assembly used. - **Always prompt user** for which columns in the methylation BED files are methylation fraction/percent and coverage and strand. - Load and preprocess CpG methylation data - Tile methylation into fixed-size windows (e.g., 1kb) or in target regions. - Import chromatin feature signal from bigWig files - Build a unified region-level integration table - Calculate correlations between every two features. - Visualization --- ## 2. When to Use This Skill Use this pipeline when you want to explore how DNA methylation relates to chromatin state, accessibility, or histone modifications. Suitable scenarios include: - Assessing promoter/enhancer activation via methylation & ATAC/H3K27ac - Integrating multi-omics datasets (ChIP-seq, ATAC-seq, WGBS) - Evaluating epigenomic shifts across conditions, tissues, or celltypes --- ## 3. Inputs & Outputs ### Inputs `<methylation_coverage>.bed` `<epi_feature_1>.bw` `<epi_feature_2>.bw` `<target_
- 1. Overview
- 2. When to Use This Skill
- 3. Inputs & Outputs
- Inputs
- Outputs
- 4. Decision Tree
- STEP 1: Prepare the sample methylation data
- STEP 3: Tile methylation into 1kb bins or count methylation in target regions
- Step 4: Build integrated region table
- STEP 6: Calculate correlations
- STEP 7: Visualization
corr_epi_methylation/ stats/ region_signal_table.tsv # Unified table of methylation + chromatin signal correlation_table.tsv # Per-feature Spearman correlations plots/ temp/
What does the correlation-methylation-epiFeatures skill do?
This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks/TF signals.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 27-correlation-methylation-epifeatures --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.