methylation-variability-analysis
This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analysis from whole-genome bisulfite sequencing (WGBS) data. It is designed for researchers who want to quantify CpG-level variability across biological samples or conditions, identify highly variable CpGs (HVCs), and explore epigenetic heterogeneity.
npx skills add majiayu000/claude-skill-registry --skill 25-methylation-variability --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.
# SKILL: Methylation Variability & Heterogeneity Analysis ## Overview Main steps include: - Refer to the **Inputs & Outputs** section to check available inputs and design the output structure. - **Always prompt user** for genome assembly used. - **Always prompt user** for which columns in the BED files are methylation fraction/percent and coverage and strand. - Building a multi-sample CpG methylation matrix from WGBS coverage files. - Computing **between-sample variability** at CpG level (variance, MAD, CV). --- ## When to use this skill Use this methylKit-based variability pipeline when you want to: - Quantify **between-sample variability** at CpG level (e.g., across replicates, cell types, conditions). - Identify **highly variable CpGs (HVCs)** as candidate epigenetically heterogeneous loci. - Explore **epigenetic heterogeneity** between groups (e.g., GM12878 vs K562, disease vs control). --- ## Inputs & Outputs ### Inputs `<sample1>.bed` `<sample2>.bed` ### Outputs ```bash methylation_variability/ stats/ top_variable_CpGs.tsv CpG_variability_stats.tsv plots/ heatmap_top_variable_CpGs.pdf distribution_CpG_variance.pdf mean_vs_variance_scatter.pdf temp/ ``` --- ## Decision Tree ##
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 1: Prepare the sample meta data
- Step 2: Statistical analysis
- Step 3: high variable CpG selection
- Step 4: Visualization
- Recommended Extensions
methylation_variability/ stats/ top_variable_CpGs.tsv CpG_variability_stats.tsv plots/ heatmap_top_variable_CpGs.pdf distribution_CpG_variance.pdf mean_vs_variance_scatter.pdf temp/
What does the methylation-variability-analysis skill do?
This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analysis from whole-genome bisulfite sequencing (WGBS) data. It is designed for researchers who want to quantify CpG-level variability across biological samples or conditions, identify highly variable CpGs (HVCs), and explore epigenetic heterogeneity.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 25-methylation-variability --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.