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Agent skill

Tooluniverse Gene Enrichment

by wu-yc in wu-yc/LabClaw

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Gene Enrichment

skills CLI
$ npx skills add wu-yc/LabClaw --skill tooluniverse-gene-enrichment -a claude-code

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

GitHub CLI
$ gh skill install wu-yc/LabClaw tooluniverse-gene-enrichment --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-gene-enrichment .claude/skills/tooluniverse-gene-enrichment && 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/

Facts

Skill name
tooluniverse-gene-enrichment
GitHub stars
1.1k
Used in
2 other repos
Token cost
~4k tokens
SKILL.md length
882 words
Files
1
Skills in repo
68
Repo updated
First seen
Licence
None found

At a glance

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.

  • Works in 5 steps: Create Report File (IMMEDIATE) → ID Conversion and Validation → Primary Enrichment with gseapy → …
  • Users ask about gene enrichment
  • SKILL.md covers When to Use This Skill, Input Parameters, Core Principles and Decision Tree: ORA vs GSEA, plus 9 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Tooluniverse Gene Enrichment is an agent skill from wu-yc/LabClaw. Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis…

Its SKILL.md is about 4k 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. It works with Ensembl, NCBI and UniProt. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists).

When your agent uses it

  • Users ask about gene enrichment
  • Pathway analysis
  • GO term enrichment
  • KEGG pathway analysis

Example prompts

  • “/tooluniverse-gene-enrichment”

Requirements

  • Python 3

Workflow steps

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

  1. Create Report File (IMMEDIATE)
  2. ID Conversion and Validation
  3. Primary Enrichment with gseapy
  4. Cross-Validation with ToolUniverse
  5. Report Compilation

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 and markdown).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • gseapy.readthedocs.io
    • pantherdb.org
    • string-db.org
    • reactome.org

    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 Gene Enrichment loads about 4k tokens when it runs. Until then it costs about 167 tokens; SKILL.md has 882 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~167
When it runs · the whole SKILL.md, loaded when a task matches
~4k

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 882 words (~3,952 tokens).

“Perform comprehensive gene enrichment analysis including Gene Ontology (GO), KEGG, Reactome, WikiPathways, and MSigDB enrichment using both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). Integrates local computation via gseapy with ToolUniverse pathway databases for cross-validated, publication-ready results.”

— opening of SKILL.md by wu-yc
name
tooluniverse-gene-enrichment

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/bio/tooluniverse-gene-enrichment 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 Gene Enrichment 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 Gene Enrichment compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tooluniverse Gene Enrichment this skillwu-yc/LabClaw1.1k2 repos~4kAutomated safety check: PassNone
Bio Biomart QueriesGPTomics/bioSkills1.2k2 repos~3.2kAutomated safety check: PassMIT
Ggetaipoch/medical-research-skills1.9k—~816Automated safety check: PassMIT
External API ChangeGuyTeichman/RNAlysis139—~1.8kAutomated safety check: PassMIT
Bio DB ToolsDrugClaw/DrugClaw126—~1.4kAutomated safety check: PassApache-2.0
Ggetdavila7/claude-code-templates33k10 repos~6.3kAutomated safety check: PassMIT

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  • Tooluniverse Drug Repurposing

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  • Tooluniverse Expression Data Retrieval

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Works with

Categories

Questions about Tooluniverse Gene Enrichment

What does Tooluniverse Gene Enrichment do?

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Tooluniverse Gene Enrichment is an agent skill from wu-yc/LabClaw. Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.

When should I use Tooluniverse Gene Enrichment?

Tooluniverse Gene Enrichment fits situations like: users ask about gene enrichment; pathway analysis; GO term enrichment; KEGG pathway analysis.

How do I install Tooluniverse Gene Enrichment in Claude Code?

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

How do I install Tooluniverse Gene Enrichment in Codex?

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

Can I use Tooluniverse Gene Enrichment 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-gene-enrichment -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-gene-enrichment, .gemini/skills/tooluniverse-gene-enrichment, .github/skills/tooluniverse-gene-enrichment and .opencode/skills/tooluniverse-gene-enrichment in your project.

What does Tooluniverse Gene Enrichment need to run?

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

Does Tooluniverse Gene Enrichment access the network?

SKILL.md names 4 domains. As links in the text: gseapy.readthedocs.io, pantherdb.org, string-db.org and reactome.org. This is read from the text; nothing was executed.

Is Tooluniverse Gene Enrichment 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 Gene Enrichment use?

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

How many tokens does Tooluniverse Gene Enrichment use?

About 4k tokens (SKILL.md is roughly 16k 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 Gene Enrichment?

Skills that share tags, products or a category with Tooluniverse Gene Enrichment: Bio Biomart Queries (GPTomics/bioSkills, 1.2k stars), Gget (aipoch/medical-research-skills, 1.9k stars), External API Change (GuyTeichman/RNAlysis, 139 stars) and Bio DB Tools (DrugClaw/DrugClaw, 126 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse Gene Enrichment?

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.