Agent skill

Tooluniverse Epigenomics

Production-ready genomics and epigenomics data processing for BixBench questions.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Epigenomics

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-epigenomics --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio/tooluniverse-epigenomics .claude/skills/tooluniverse-epigenomics && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "tooluniverse-epigenomics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics into .claude/skills/tooluniverse-epigenomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-epigenomics", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-epigenomics --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio/tooluniverse-epigenomics .agents/skills/tooluniverse-epigenomics && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "tooluniverse-epigenomics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics into .agents/skills/tooluniverse-epigenomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-epigenomics", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-epigenomics --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio/tooluniverse-epigenomics .cursor/skills/tooluniverse-epigenomics && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "tooluniverse-epigenomics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics into .cursor/skills/tooluniverse-epigenomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-epigenomics", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/wu-yc/LabClaw.git --path skills/bio/tooluniverse-epigenomics

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-epigenomics --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio/tooluniverse-epigenomics .gemini/skills/tooluniverse-epigenomics && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "tooluniverse-epigenomics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics into .gemini/skills/tooluniverse-epigenomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-epigenomics", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-epigenomics

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio/tooluniverse-epigenomics .github/skills/tooluniverse-epigenomics && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "tooluniverse-epigenomics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics into .github/skills/tooluniverse-epigenomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-epigenomics", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw tooluniverse-epigenomics --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio/tooluniverse-epigenomics .opencode/skills/tooluniverse-epigenomics && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "tooluniverse-epigenomics" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/bio/tooluniverse-epigenomics into .opencode/skills/tooluniverse-epigenomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse-epigenomics", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: tooluniverse-epigenomics
GitHub stars: 1.1k
Used in: 2 other repos
Token cost: ~14k tokens
SKILL.md length: 1,324 words
Files: 1
Skills in repo: 68
Repo updated: Mar 19, 2026
First seen: Oct 7, 2026
Licence: None found

At a glance

Production-ready genomics and epigenomics data processing for BixBench questions.

Works in 8 steps: Question Parsing and Data Discovery → Methylation Data Processing → ChIP-seq Peak Analysis → …
Processing methylation data
SKILL.md covers When to Use This Skill, Required Python Packages, KEY PRINCIPLES and Complete Workflow, plus 5 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Tooluniverse Epigenomics is an agent skill from wu-yc/LabClaw. Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse annotation tools…

Its SKILL.md is about 14k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics and Statistics. It works with Python, NumPy, pandas and pysam. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists).

When your agent uses it

Processing methylation data
ATAC-seq signals
Answering questions about CpG sites
Differential methylation

Example prompts

“/tooluniverse-epigenomics”

Requirements

Python 3

Workflow steps

8 steps, taken from the step headings in SKILL.md.

Question Parsing and Data Discovery
Methylation Data Processing
ChIP-seq Peak Analysis
ATAC-seq Analysis
Multi-Omics Integration
Clinical Data Integration
ToolUniverse Annotation Integration
Genome-Wide Statistics

What it can do on your machine

Read from SKILL.md and the folder at commit df37802. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Tooluniverse Epigenomics loads about 14k tokens when it runs. Until then it costs about 230 tokens; SKILL.md has 1,324 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~230
When it runs · the whole SKILL.md, loaded when a task matches: ~14k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 1,324 words (~13,679 tokens).

“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.”

— opening of SKILL.md by wu-yc

name: tooluniverse-epigenomics

Outline of SKILL.md

Genomics and Epigenomics Data Processing
When to Use This Skill
Required Python Packages
KEY PRINCIPLES
Complete Workflow
Phase 0: Question Parsing and Data Discovery
Phase 1: Methylation Data Processing
Phase 2: ChIP-seq Peak Analysis
Phase 3: ATAC-seq Analysis
Phase 4: Multi-Omics Integration
Phase 5: Clinical Data Integration
Phase 6: ToolUniverse Annotation Integration
Phase 7: Genome-Wide Statistics
ToolUniverse Tool Parameter Reference
Regulatory Annotation Tools
Gene Annotation Tools
CRITICAL Tool Notes
Response Format Notes
Fallback Strategies
Common Use Patterns
Pattern 1: Methylation Array Analysis
Pattern 2: Age-Related CpG Density
Pattern 3: Multi-Omics Missing Data
Pattern 4: ChIP-seq Peak Annotation
Pattern 5: Methylation-Expression Integration
Edge Cases
Missing Probe Annotation
Mixed Genome Builds
Very Large Datasets
Sample ID Mismatches

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/bio/tooluniverse-epigenomics of wu-yc/LabClaw.

Open the folder on GitHubat commit df37802

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in wu-yc/LabClaw, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Tooluniverse Epigenomics next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Tooluniverse Epigenomics compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Tooluniverse Epigenomics this skillwu-yc/LabClaw	1.1k	2 repos	~14k	Automated safety check: Pass	None	6 mo ago
Statistical Data Analysislingzhi227/agent-research-skills	390	—	~886	Automated safety check: Pass	None	7 mo ago
PyDESeq2 Differential Expressiondavila7/claude-code-templates	33k	11 repos	~4k	Automated safety check: Pass	MIT	today
Bio Temporal Genomics Temporal GrnGPTomics/bioSkills	1.2k	1 repos	~5k	Automated safety check: Pass	MIT	1 mo ago
Bio Workflows Timecourse PipelineGPTomics/bioSkills	1.2k	1 repos	~6k	Automated safety check: Pass	MIT	1 mo ago
Bio Proteomics Differential AbundanceFreedomIntelligence/OpenClaw-Medical-Skills	3.1k	—	~1.2k	Automated safety check: Pass	None	2 mo ago

Similar skills

Statistical Data Analysis
lingzhi227/agent-research-skills
Writes statistical analysis code for experimental data, runs it through a four-round review, and reports effect sizes, p-values and confidence intervals.
390 GitHub stars~886 tokensUpdated 7 mo ago
Data & AnalyticsAuto-check passed
PyDESeq2 Differential Expression
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
33k GitHub starsUsed in 11 repos~4k tokens
Research & ScienceAuto-check passed
Bio Temporal Genomics Temporal Grn
GPTomics/bioSkills
Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives…
1.2k GitHub starsUsed in 1 repo~5k tokens
Research & ScienceAuto-check passed
Bio Workflows Timecourse Pipeline
GPTomics/bioSkills
End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment.
1.2k GitHub starsUsed in 1 repo~6k tokens
Research & ScienceAuto-check passed
Bio Proteomics Differential Abundance
FreedomIntelligence/OpenClaw-Medical-Skills
Statistical testing for differentially abundant proteins between conditions.
3.1k GitHub stars~1.2k tokensUpdated 2 mo ago
Research & ScienceAuto-check passed
Q-EDA Exploratory Analysis
TyrealQ/q-skills
Runs exploratory data analysis on tabular data after you confirm each column's measurement level, then writes CSV tables and a narrative summary.
108 GitHub stars~1.1k tokensUpdated 17 days ago
Data & AnalyticsAuto-check passed

More from wu-yc/LabClaw

All 68 skills in this repo

Tooluniverse Chemical Compound Retrieval
wu-yc/LabClaw
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment.
1.1k GitHub starsUsed in 2 repos~2.3k tokens
Auto-check passed
Tooluniverse Clinical Guidelines
wu-yc/LabClaw
Search and retrieve clinical practice guidelines across 12+ authoritative sources including NICE, WHO, ADA, AHA/ACC, NCCN, SIGN, CPIC, CMA, CTFPHC, GIN, MAGICapp, PubMed, EuropePMC, TRIP, and…
1.1k GitHub starsUsed in 2 repos~4.9k tokens
Auto-check passed
Tooluniverse Disease Research
wu-yc/LabClaw
Generate comprehensive disease research reports using 100+ ToolUniverse tools.
1.1k GitHub starsUsed in 2 repos~4.7k tokens
Auto-check passed
Tooluniverse Drug Repurposing
wu-yc/LabClaw
Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies.
1.1k GitHub starsUsed in 2 repos~4.4k tokens
Auto-check passed
Tooluniverse Expression Data Retrieval
wu-yc/LabClaw
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports.
1.1k GitHub starsUsed in 2 repos~2.6k tokens
Auto-check passed
Tooluniverse Gene Enrichment
wu-yc/LabClaw
Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.
1.1k GitHub starsUsed in 2 repos~4k tokens
Auto-check passed

Works with

Questions about Tooluniverse Epigenomics

What does Tooluniverse Epigenomics do?

Production-ready genomics and epigenomics data processing for BixBench questions. Tooluniverse Epigenomics is an agent skill from wu-yc/LabClaw. Production-ready genomics and epigenomics data processing for BixBench questions.

When should I use Tooluniverse Epigenomics?

Tooluniverse Epigenomics fits situations like: processing methylation data; ATAC-seq signals; answering questions about CpG sites; differential methylation.

How do I install Tooluniverse Epigenomics in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a claude-code`. Or copy the skill folder (skills/bio/tooluniverse-epigenomics in wu-yc/LabClaw) into .claude/skills/tooluniverse-epigenomics in your project. Claude Code loads it when a task matches its description.

How do I install Tooluniverse Epigenomics in Codex?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a codex`. Or copy the skill folder (skills/bio/tooluniverse-epigenomics in wu-yc/LabClaw) into .agents/skills/tooluniverse-epigenomics in your project. Codex loads it when a task matches its description.

Can I use Tooluniverse Epigenomics in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wu-yc/LabClaw --skill tooluniverse-epigenomics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tooluniverse-epigenomics, .gemini/skills/tooluniverse-epigenomics, .github/skills/tooluniverse-epigenomics and .opencode/skills/tooluniverse-epigenomics in your project.

What does Tooluniverse Epigenomics need to run?

SKILL.md names no scripts, command-line tools or credentials: Tooluniverse Epigenomics is instructions for the agent only. Our summary lists: Python 3.

Does Tooluniverse Epigenomics access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Tooluniverse Epigenomics safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Tooluniverse Epigenomics use?

No licence was found for Tooluniverse Epigenomics or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Tooluniverse Epigenomics use?

About 14k tokens (SKILL.md is roughly 55k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Tooluniverse Epigenomics?

Skills that share tags, products or a category with Tooluniverse Epigenomics: Statistical Data Analysis (lingzhi227/agent-research-skills, 390 stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 33k stars), Bio Temporal Genomics Temporal Grn (GPTomics/bioSkills, 1.2k stars) and Bio Workflows Timecourse Pipeline (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse Epigenomics?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,055 GitHub stars. The repository holds 68 skills in this directory. The repository was last updated on March 19, 2026.

Source: wu-yc/LabClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Tooluniverse Epigenomics

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from wu-yc/LabClaw

Related

Questions about Tooluniverse Epigenomics