bio-methylation-differential-cpg
Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage filtering, statistical tests (Welch t-test, Mann-Whitney, limma, DSS beta-binomial), multiple testing correction, and effect size calculation. Use when comparing methylation at individual CpG sites between experimental groups from WGBS, RRBS, or targeted bisulfite sequencing.
npx skills add BioTender-max/awesome-bio-agent-skills --skill differential-cpg-testing --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.
## Version Compatibility Reference examples tested with: scipy 1.12+, statsmodels 0.14+, pandas 2.2+, numpy 1.26+, limma 3.58+, DSS 2.50+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Per-CpG Differential Methylation Testing **"Test individual CpG sites for differential methylation between groups"** -> Compute per-CpG methylation metrics from count data, apply coverage filters, run statistical tests for group differences, correct for multiple testing, and report effect sizes. - Python: `scipy.stats.ttest_ind()` + `statsmodels.stats.multitest.multipletests()` - R: `limma::lmFit()` + `eBayes()` on M-values, `DSS::DMLtest()` on counts ## Beta Values and M-Values **Goal:** Convert raw bisulfite sequencing count data into analyzable methylation metrics. **Approach:** Compute beta values (methylation proportion) for biological interpretation an
- Version Compatibility
- Beta Values and M-Values
- Coverage Filtering
- Coverage Thresholds by Assay
- Method Selection
- Fisher's Exact Test (Python, Unreplicated Only)
- Welch's t-Test on Beta Values (Python)
- Mann-Whitney U Test (Python)
- limma on M-Values (R)
- DSS Beta-Binomial Model (R)
- Effect Size Calculation
- Effect Size Thresholds
- Full Python Pipeline
- Common Pitfalls
What does the bio-methylation-differential-cpg skill do?
Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage filtering, statistical tests (Welch t-test, Mann-Whitney, limma, DSS beta-binomial), multiple testing correction, and effect size calculation. Use when comparing methylation at individual CpG sites between experimental groups from WGBS, RRBS, or targeted bisulfite sequencing.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill differential-cpg-testing --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.