Pathway Enrichment
K-Dense-AI/scientific-agent-skills
Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results.
Agent skill
Gsea Enrichment Analysis
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Gene set enrichment analysis with correct geneset format handling.
No licenceAuto-check passed
Install Gsea Enrichment Analysis
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills gsea-enrichment-analysis --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gsea-enrichment .claude/skills/gsea-enrichment-analysis && rm -rf skills-srcUse ~/.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/
Install the "gsea-enrichment-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment into .claude/skills/gsea-enrichment-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gsea-enrichment-analysis", 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 install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichmentType 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.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills gsea-enrichment-analysis --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/gsea-enrichment .agents/skills/gsea-enrichment-analysis && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "gsea-enrichment-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment into .agents/skills/gsea-enrichment-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gsea-enrichment-analysis", 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.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills gsea-enrichment-analysis --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/gsea-enrichment .cursor/skills/gsea-enrichment-analysis && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "gsea-enrichment-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment into .cursor/skills/gsea-enrichment-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gsea-enrichment-analysis", 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 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/gsea-enrichment--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills gsea-enrichment-analysis --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/gsea-enrichment .gemini/skills/gsea-enrichment-analysis && rm -rf skills-srcUse ~/.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/
Install the "gsea-enrichment-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment into .gemini/skills/gsea-enrichment-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gsea-enrichment-analysis", 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.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills gsea-enrichment-analysisInstalls 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).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/gsea-enrichment .github/skills/gsea-enrichment-analysis && rm -rf skills-srcUse ~/.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/
Install the "gsea-enrichment-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment into .github/skills/gsea-enrichment-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gsea-enrichment-analysis", 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.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills gsea-enrichment-analysis --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gsea-enrichment .opencode/skills/gsea-enrichment-analysis && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "gsea-enrichment-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment into .opencode/skills/gsea-enrichment-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gsea-enrichment-analysis", 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
gsea-enrichment-analysis- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.3k tokens
- SKILL.md length
- 307 words
- Files
- 1
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Gene set enrichment analysis with correct geneset format handling.
- Works in 5 steps: Always load genesets first: Never pass… → Check gene format: Ensure gene symbols… → Download once: Run… → …
- SKILL.md covers Overview, Critical API Reference -…, Common Errors and Solutions and Pathway Databases Available, plus 3 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Gsea Enrichment Analysis is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
Example prompts
- “/gsea-enrichment-analysis”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Always load genesets first: Never pass file paths directly to geneset_enrichment()
- Check gene format: Ensure gene symbols match (CAPS for human, Title case for mouse)
- Download once: Run download_pathway_database() once per environment
- Specify organism: Always set organism='Human' or organism='Mouse'
- Use background genes: For more accurate results, provide background parameter
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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
Gsea Enrichment Analysis loads about 1.3k tokens when it runs. Until then it costs about 44 tokens; SKILL.md has 307 words of instructions outside code blocks.
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 307 words (~1,334 tokens).
“This skill covers gene set enrichment analysis (GSEA) and pathway enrichment workflows in OmicVerse. It provides critical guidance on the correct data formats and API usage patterns to avoid common errors.”
- name
- gsea-enrichment-analysis
- title
- GSEA and Pathway Enrichment Analysis
Files
Just SKILL.md in skills/gsea-enrichment of FreedomIntelligence/OpenClaw-Medical-Skills.
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Gsea Enrichment Analysis 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Gsea Enrichment Analysis this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.3k | Automated safety check: Pass | None | |
| Pathway EnrichmentK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.2k | Automated safety check: Pass | MIT | |
| Tooluniverse Gene Enrichmentwu-yc/LabClaw | 1.1k | 2 repos | ~4k | Automated safety check: Pass | None | |
| Gseaaipoch/medical-research-skills | 1.9k | — | ~2.2k | Automated safety check: Pass | MIT | |
| Correctcursor/plugins | 11k | 3 repos | ~612 | Automated safety check: Pass | None | |
| CorrectionNxcoreAI/EverRoom | 3k | — | ~290 | Automated safety check: Pass | Custom licence |
Similar skills
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.
Gsea
aipoch/medical-research-skills
Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.
- Official
Correct
cursor/plugins
Find the mistakes agents keep repeating in this repo and make each one impossible.
Correction
NxcoreAI/EverRoom
Compute Room overview corrections—citation corrections as per-claim edits and general corrections as a single proposal.
Add Enrichment
simstudioai/sim
Add a code-defined table enrichment (registry entry) under apps/sim/enrichments/ backed by an ordered provider cascade, ensuring every provider tool it calls has hosted-key support.
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Questions about Gsea Enrichment Analysis
What does Gsea Enrichment Analysis do?
Gene set enrichment analysis with correct geneset format handling. Gsea Enrichment Analysis is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Gene set enrichment analysis with correct geneset format handling.
How do I install Gsea Enrichment Analysis in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a claude-code`. Or copy the skill folder (skills/gsea-enrichment in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/gsea-enrichment-analysis in your project. Claude Code loads it when a task matches its description.
How do I install Gsea Enrichment Analysis in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a codex`. Or copy the skill folder (skills/gsea-enrichment in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/gsea-enrichment-analysis in your project. Codex loads it when a task matches its description.
Can I use Gsea Enrichment Analysis 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill gsea-enrichment-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gsea-enrichment-analysis, .gemini/skills/gsea-enrichment-analysis, .github/skills/gsea-enrichment-analysis and .opencode/skills/gsea-enrichment-analysis in your project.
What does Gsea Enrichment Analysis need to run?
SKILL.md names no scripts, command-line tools or credentials: Gsea Enrichment Analysis is instructions for the agent only. Our summary lists: Python 3.
Does Gsea Enrichment Analysis 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 Gsea Enrichment Analysis 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 Gsea Enrichment Analysis use?
No licence was found for Gsea Enrichment Analysis or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Gsea Enrichment Analysis use?
About 1.3k tokens (SKILL.md is roughly 5.3k 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 Gsea Enrichment Analysis?
Skills that share tags, products or a category with Gsea Enrichment Analysis: Pathway Enrichment (K-Dense-AI/scientific-agent-skills, 48k stars), Tooluniverse Gene Enrichment (wu-yc/LabClaw, 1.1k stars), Gsea (aipoch/medical-research-skills, 1.9k stars) and Correct (cursor/plugins, 11k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Gsea Enrichment Analysis?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.