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
Bio Pathway Wikipathways
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
WikiPathways enrichment using clusterProfiler and rWikiPathways.
No licenceAuto-check passed
Install Bio Pathway Wikipathways
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-wikipathways -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pathway-wikipathways --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/bio-pathway-wikipathways .claude/skills/bio-pathway-wikipathways && 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 "bio-pathway-wikipathways" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways into .claude/skills/bio-pathway-wikipathways/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pathway-wikipathways", 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/bio-pathway-wikipathwaysType 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 bio-pathway-wikipathways -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pathway-wikipathways --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/bio-pathway-wikipathways .agents/skills/bio-pathway-wikipathways && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-pathway-wikipathways" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways into .agents/skills/bio-pathway-wikipathways/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pathway-wikipathways", 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 bio-pathway-wikipathways -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pathway-wikipathways --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/bio-pathway-wikipathways .cursor/skills/bio-pathway-wikipathways && 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 "bio-pathway-wikipathways" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways into .cursor/skills/bio-pathway-wikipathways/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pathway-wikipathways", 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/bio-pathway-wikipathways--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 bio-pathway-wikipathways -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pathway-wikipathways --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/bio-pathway-wikipathways .gemini/skills/bio-pathway-wikipathways && 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 "bio-pathway-wikipathways" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways into .gemini/skills/bio-pathway-wikipathways/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pathway-wikipathways", 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 bio-pathway-wikipathwaysInstalls 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 bio-pathway-wikipathways -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/bio-pathway-wikipathways .github/skills/bio-pathway-wikipathways && 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 "bio-pathway-wikipathways" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways into .github/skills/bio-pathway-wikipathways/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pathway-wikipathways", 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 bio-pathway-wikipathways -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 bio-pathway-wikipathways --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/bio-pathway-wikipathways .opencode/skills/bio-pathway-wikipathways && 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 "bio-pathway-wikipathways" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways into .opencode/skills/bio-pathway-wikipathways/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pathway-wikipathways", 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
bio-pathway-wikipathways- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.7k tokens
- SKILL.md length
- 401 words
- Files
- 4
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
WikiPathways enrichment using clusterProfiler and rWikiPathways.
- Analyzing gene lists against community-curated open-source pathways
- SKILL.md covers Version Compatibility, Core Pattern -…, Prepare Gene List and GSEA on WikiPathways, plus 12 more sections
- Runs R scripts from its folder
What it does
Bio Pathway Wikipathways is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Analyzing gene lists against community-curated open-source pathways
Example prompts
- “Use the bio-pathway-wikipathways skill to wikipathway enrichment using clusterProfiler and rWikiPathways”
- “/bio-pathway-wikipathways”
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
Ships script files (R), which the agent can run.
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
Bio Pathway Wikipathways loads about 1.7k tokens when it runs. Until then it costs about 58 tokens; SKILL.md has 401 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 401 words (~1,728 tokens).
“Reference examples tested with: ReactomePA 1.46+, clusterProfiler 4.10+, rWikiPathways 1.24+”
- name
- bio-pathway-wikipathways
- tool_type
- r
- primary_tool
- clusterProfiler
Files
SKILL.md and 3 other files in skills/bio-pathway-wikipathways of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/wikipathways_explore.R
- examples/wikipathways_ora.R
- usage-guide.md
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
Bio Pathway Wikipathways 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 |
|---|---|---|---|---|---|---|
| Bio Pathway Wikipathways this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.7k | Automated safety check: Pass | None | |
| Pathway EnrichmentK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.2k | Automated safety check: Pass | MIT | |
| Bio Pathway WikipathwaysGPTomics/bioSkills | 1.2k | 1 repos | ~4.5k | Automated safety check: Pass | MIT | |
| Bio Pathway Go EnrichmentGPTomics/bioSkills | 1.2k | 1 repos | ~5.1k | Automated safety check: Pass | MIT | |
| Bio Pathway Kegg PathwaysGPTomics/bioSkills | 1.2k | 1 repos | ~5.4k | Automated safety check: Pass | MIT | |
| Bio Pathway Enrichment VisualizationGPTomics/bioSkills | 1.2k | 1 repos | ~5.6k | Automated safety check: Pass | MIT |
Similar skills
Bio Pathway Wikipathways
GPTomics/bioSkills
Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways.
Bio Pathway Go Enrichment
GPTomics/bioSkills
Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE).
Bio Pathway Kegg Pathways
GPTomics/bioSkills
Tests gene lists, ranked vectors, and fold-change vectors against KEGG pathways and modules with clusterProfiler enrichKEGG/enrichMKEGG (ORA), gseKEGG (GSEA), and SPIA/graphite (signed-topology…
Bio Pathway Enrichment Visualization
GPTomics/bioSkills
Turns an enrichResult or gseaResult from clusterProfiler/enrichplot into a figure that collapses or shows gene-set redundancy, using dotplot, barplot, cnetplot, emapplot, treeplot, ridgeplot…
Pathway Enricher
ClawBio/ClawBio
Gene-set pathway enrichment analysis using Enrichr — queries KEGG, GO (BP/MF/CC), Reactome, WikiPathways, MSigDB, and Disease Ontology.
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Questions about Bio Pathway Wikipathways
What does Bio Pathway Wikipathways do?
WikiPathways enrichment using clusterProfiler and rWikiPathways. Bio Pathway Wikipathways is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. WikiPathways enrichment using clusterProfiler and rWikiPathways.
When should I use Bio Pathway Wikipathways?
Bio Pathway Wikipathways fits situations like: analyzing gene lists against community-curated open-source pathways.
How do I install Bio Pathway Wikipathways in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-wikipathways -a claude-code`. Or copy the skill folder (skills/bio-pathway-wikipathways in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-pathway-wikipathways in your project. Claude Code loads it when a task matches its description.
How do I install Bio Pathway Wikipathways in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-wikipathways -a codex`. Or copy the skill folder (skills/bio-pathway-wikipathways in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-pathway-wikipathways in your project. Codex loads it when a task matches its description.
Can I use Bio Pathway Wikipathways 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 bio-pathway-wikipathways -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-pathway-wikipathways, .gemini/skills/bio-pathway-wikipathways, .github/skills/bio-pathway-wikipathways and .opencode/skills/bio-pathway-wikipathways in your project.
What does Bio Pathway Wikipathways need to run?
Going by SKILL.md and its folder, Bio Pathway Wikipathways needs R for the scripts in its folder.
Does Bio Pathway Wikipathways 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 Bio Pathway Wikipathways 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 Bio Pathway Wikipathways use?
No licence was found for Bio Pathway Wikipathways or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Pathway Wikipathways use?
About 1.7k tokens (SKILL.md is roughly 6.9k 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 Bio Pathway Wikipathways?
Skills that share tags, products or a category with Bio Pathway Wikipathways: Pathway Enrichment (K-Dense-AI/scientific-agent-skills, 48k stars), Bio Pathway Wikipathways (GPTomics/bioSkills, 1.2k stars), Bio Pathway Go Enrichment (GPTomics/bioSkills, 1.2k stars) and Bio Pathway Kegg Pathways (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 Bio Pathway Wikipathways?
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.