Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add AndyZhuang/Opentest --skill tooluniverse-epigenomicsgit clone --depth 1 https://github.com/AndyZhuang/OpentestWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-epigenomics)<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-epigenomics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-epigenomics/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-epigenomics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-epigenomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00205 | $0.13784 |
| Opus 5 | $0.00102 | $0.06892 |
| Sonnet 5 | $0.00041 | $0.02757 |
| Haiku 4.5 | $0.00020 | $0.01378 |
Grade A, and why
tooluniverse-epigenomics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 1,490 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Genomics and Epigenomics Data Processing
Production-ready computational skill for processing and analyzing epigenomics data. Combines local Python computation (pandas, scipy, numpy, pysam, statsmodels) with ToolUniverse annotation tools for regulatory context. Designed to solve BixBench-style questions about methylation, ChIP-seq, ATAC-seq, and multi-omics integration.
When to Use This Skill
Triggers:
- User provides methylation data (beta-value matrices, Illumina arrays) and asks about CpG sites
- Questions about differential methylation analysis
- Age-related CpG detection or epigenetic clock questions
- Chromosome-level methylation density or statistics
- ChIP-seq peak files (BED format) with analysis questions
- ATAC-seq chromatin accessibility questions
- Multi-omics integration (expression + methylation, expression + ChIP-seq)
- Genome-wide epigenomic statistics
- Questions mentioning "methylation", "CpG", "ChIP-seq", "ATAC-seq", "histone", "chromatin", "epigenetic"
- Questions about missing data across clinical/genomic/epigenomic modalities
- Regulatory element annotation for processed epigenomic data
Example Questions This Skill Solves:
- "How many patients have no missing data for vital status, gene expression, and methylation data?"
- "What is the ratio of filtered age-related CpG density between chromosomes?"
- "What is the genome-wide average chromosomal density of unique age-related CpGs per base pair?"
- "How many CpG sites show significant differential methylation (padj < 0.05)?"
- "What is the Pearson correlation between methylation and expression for gene X?"
- "How many ChIP-seq peaks overlap with promoter regions?"
- "What fraction of ATAC-seq peaks are in enhancer regions?"
- "Which chromosome has the highest density of hypermethylated CpGs?"
- "Filter CpG sites by variance > threshold and map to nearest genes"
- "What is the average beta value difference between tumor and normal for chromosome 17?"
NOT for (use other skills instead):
- Gene regulation lookup without data files -> Use existing epigenomics annotation pattern
- RNA-seq differential expression -> Use
tooluniverse-rnaseq-deseq2 - Variant calling/annotation from VCF -> Use
tooluniverse-variant-analysis - Gene enrichment analysis -> Use
tooluniverse-gene-enrichment - Protein structure analysis -> Use
tooluniverse-protein-structure-retrieval
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 11d ago First seen · 1,490 lines · 205 tokens per session scan A 4e1ba0e6d4fe
tooluniverse-epigenomics is a skill published in the GitHub repository AndyZhuang/Opentest (22 stars, last pushed 6mo ago), licensed MIT. It adds 205 tokens to every session and 13,784 once invoked, about $0.0010 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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