Mcpmed Bioinformatics Server
FreedomIntelligence/OpenClaw-Medical-Skills
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration.
Install Kegg Analysis
$ npx skills add davepoon/buildwithclaude --skill kegg-analysis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install davepoon/buildwithclaude kegg-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/davepoon/buildwithclaude.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugins/kegg-mcp-server/skills/kegg-analysis .claude/skills/kegg-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 "kegg-analysis" agent skill from https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis into .claude/skills/kegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "kegg-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/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysisType 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 davepoon/buildwithclaude --skill kegg-analysis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install davepoon/buildwithclaude kegg-analysis --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/davepoon/buildwithclaude.git skills-src && mkdir -p .agents/skills && cp -r skills-src/plugins/kegg-mcp-server/skills/kegg-analysis .agents/skills/kegg-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 "kegg-analysis" agent skill from https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis into .agents/skills/kegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "kegg-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 davepoon/buildwithclaude --skill kegg-analysis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install davepoon/buildwithclaude kegg-analysis --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/davepoon/buildwithclaude.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/plugins/kegg-mcp-server/skills/kegg-analysis .cursor/skills/kegg-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 "kegg-analysis" agent skill from https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis into .cursor/skills/kegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "kegg-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/davepoon/buildwithclaude.git --path plugins/kegg-mcp-server/skills/kegg-analysis--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 davepoon/buildwithclaude --skill kegg-analysis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install davepoon/buildwithclaude kegg-analysis --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/davepoon/buildwithclaude.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/plugins/kegg-mcp-server/skills/kegg-analysis .gemini/skills/kegg-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 "kegg-analysis" agent skill from https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis into .gemini/skills/kegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "kegg-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 davepoon/buildwithclaude kegg-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 davepoon/buildwithclaude --skill kegg-analysis -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/davepoon/buildwithclaude.git skills-src && mkdir -p .github/skills && cp -r skills-src/plugins/kegg-mcp-server/skills/kegg-analysis .github/skills/kegg-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 "kegg-analysis" agent skill from https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis into .github/skills/kegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "kegg-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 davepoon/buildwithclaude --skill kegg-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 davepoon/buildwithclaude kegg-analysis --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/davepoon/buildwithclaude.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/plugins/kegg-mcp-server/skills/kegg-analysis .opencode/skills/kegg-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 "kegg-analysis" agent skill from https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis into .opencode/skills/kegg-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "kegg-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
kegg-analysis- GitHub stars
- 3.6k
- Token cost
- ~979 tokens
- SKILL.md length
- 346 words
- Files
- 1
- Skills in repo
- 246
- Repo updated
- First seen
- Licence
- MIT
At a glance
Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration.
- Works in 5 steps: Identifies the analysis type from the… → Resolves identifiers — maps gene… → Retrieves cross-linked data — follows… → …
- Tasks that involve Bioinformatics
- SKILL.md covers When to Use This Skill, What This Skill Does, How to Use and Example, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Kegg Analysis is an agent skill from davepoon/buildwithclaude. Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration. Guides Claude through the full analytical pipeline using KEGG MCP tools.
Its SKILL.md is about 980 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 MCP servers. The repository describes itself as: A single hub to find Claude Skills, Agents, Commands, Hooks, Plugins, and Marketplace collections to extend Claude Code, Claude Desktop, Agent SDK and OpenClaw. The licence is MIT.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve MCP servers
Example prompts
- “/kegg-analysis”
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Identifies the analysis type from the user's input (enrichment, drug, comparison, network)
- Resolves identifiers — maps gene symbols, drug names, or pathway IDs to KEGG entries
- Retrieves cross-linked data — follows relationships across KEGG databases
- Aggregates and ranks results — counts pathway hits, scores conservation, groups by function
- Synthesizes biological context — explains significance, not just IDs
What it can do on your machine
Read from SKILL.md and the folder at commit 616deb5. 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.
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
Kegg Analysis loads about 979 tokens when it runs. Until then it costs about 68 tokens; SKILL.md has 346 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
The full file from davepoon/buildwithclaude at commit 616deb5, republished under its MIT licence (© davepoon). 346 words, ~979 tokens.
Download SKILL.mdSave it as
.claude/skills/kegg-analysis/SKILL.md (or your agent's skills folder).- name
- kegg-analysis
- description
- Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration. Guides Claude through the full analytical pipeline using KEGG MCP tools.
- category
- data-ai
KEGG Bioinformatics Analysis
This skill orchestrates multi-step biological analyses using the KEGG MCP server tools. It transforms raw gene lists, drug names, or pathway IDs into structured biological insights.
When to Use This Skill
- Performing pathway enrichment analysis on a gene list
- Investigating a drug's mechanism of action, targets, and interactions
- Comparing metabolic pathways across species
- Tracing compound-reaction networks
- Mapping genes to functional modules and ortholog groups
What This Skill Does
- Identifies the analysis type from the user's input (enrichment, drug, comparison, network)
- Resolves identifiers — maps gene symbols, drug names, or pathway IDs to KEGG entries
- Retrieves cross-linked data — follows relationships across KEGG databases
- Aggregates and ranks results — counts pathway hits, scores conservation, groups by function
- Synthesizes biological context — explains significance, not just IDs
How to Use
Pathway Enrichment
Analyze these genes for pathway enrichment in human: BRCA1, TP53, EGFR, KRAS, PIK3CAWorkflow:
search_genesfor each gene in the target organism (e.g., hsa)get_gene_infoto confirm identity and get KEGG gene IDsfind_related_entriesto get pathway associations per gene- Aggregate: count how many input genes map to each pathway
get_pathway_infofor top pathwaysrender_pathway_asciifor visual context- Report ranked pathways with p-value proxy (gene count / pathway size)
Drug Target Investigation
Investigate metformin: targets, pathways, and interactionsWorkflow:
search_drugsto find the KEGG drug entryget_drug_infofor targets, classification, and metabolismsearch_genesfor each target genefind_related_entriesto get target pathwaysget_drug_interactionsfor DDI screening- Synthesize mechanism-of-action summary
Cross-Species Comparison
Compare glycolysis (map00010) between human, E. coli, and yeastWorkflow:
get_pathway_infofor organism-specific variants (hsa00010, eco00010, sce00010)get_pathway_genesfor each organismget_gene_orthologsto identify conserved vs. species-specific enzymesget_pathway_compoundsto compare metabolite poolsrender_pathway_asciifor each organism- Report conservation matrix and unique adaptations
Example
User: "What pathways are enriched in this gene set: SOD1, SOD2, CAT, GPX1, PRDX1?"
Output:
Pathway Enrichment Results (Homo sapiens)
Top Pathways:
1. hsa04146 Peroxisome (4/5 genes) — organelle for fatty acid oxidation and ROS detox
2. hsa04216 Ferroptosis (3/5 genes) — iron-dependent cell death regulated by GPX
3. hsa05022 Pathways of neurodegeneration (3/5 genes) — oxidative damage in ALS, AD, PD
4. hsa00480 Glutathione metabolism (2/5 genes) — GSH-dependent antioxidant system
Biological Context:
All 5 genes encode antioxidant enzymes. The enrichment in Peroxisome
and Ferroptosis pathways reflects their central role in reactive oxygen
species (ROS) detoxification. The neurodegeneration hit is consistent
with oxidative stress as a driver of SOD1-linked ALS.Tips
- Provide organism context (human, mouse, E. coli) for faster resolution
- Use standard gene symbols — KEGG resolves HGNC symbols for human
- For large gene lists (>20), batch with
batch_entry_lookup(max 50 per call) - Cross-reference with
convert_identifiersto bridge UniProt, NCBI Gene, or PDB IDs - Use
find_related_entriesto discover unexpected connections between databases
© davepoon, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in plugins/kegg-mcp-server/skills/kegg-analysis of davepoon/buildwithclaude.
Open the folder on GitHubat commit 616deb5
Compare with similar skills
Kegg 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 |
|---|---|---|---|---|---|---|
| Kegg Analysis this skilldavepoon/buildwithclaude | 3.6k | — | ~979 | Automated safety check: Pass | MIT | |
| Mcpmed Bioinformatics ServerFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~353 | Automated safety check: Pass | MIT | |
| Hcls Build Agentaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | — | ~885 | Automated safety check: Pass | MIT-0 | |
| Genomic IntelligenceK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~6.2k | Automated safety check: Notes | MIT | |
| Research Biomedical Databasesaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | — | ~3.1k | Automated safety check: Pass | MIT-0 | |
| Bioqc MCPClawBio/ClawBio | 1.2k | — | ~2.2k | Automated safety check: Pass | MIT |
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Questions about Kegg Analysis
What does Kegg Analysis do?
Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration. Kegg Analysis is an agent skill from davepoon/buildwithclaude. Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration.
When should I use Kegg Analysis?
Kegg Analysis fits situations like: tasks that involve Bioinformatics; tasks that involve MCP servers.
How do I install Kegg Analysis in Claude Code?
Run `npx skills add davepoon/buildwithclaude --skill kegg-analysis -a claude-code`. Or copy the skill folder (plugins/kegg-mcp-server/skills/kegg-analysis in davepoon/buildwithclaude) into .claude/skills/kegg-analysis in your project. Claude Code loads it when a task matches its description.
How do I install Kegg Analysis in Codex?
Run `npx skills add davepoon/buildwithclaude --skill kegg-analysis -a codex`. Or copy the skill folder (plugins/kegg-mcp-server/skills/kegg-analysis in davepoon/buildwithclaude) into .agents/skills/kegg-analysis in your project. Codex loads it when a task matches its description.
Can I use Kegg 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 davepoon/buildwithclaude --skill kegg-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/kegg-analysis, .gemini/skills/kegg-analysis, .github/skills/kegg-analysis and .opencode/skills/kegg-analysis in your project.
What does Kegg Analysis need to run?
SKILL.md names no scripts, command-line tools or credentials: Kegg Analysis is instructions for the agent only.
Does Kegg 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 Kegg 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 Kegg Analysis use?
Kegg Analysis is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Kegg Analysis use?
About 979 tokens (SKILL.md is roughly 3.9k 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 Kegg Analysis?
Skills that share tags, products or a category with Kegg Analysis: Mcpmed Bioinformatics Server (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Hcls Build Agent (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Genomic Intelligence (K-Dense-AI/scientific-agent-skills, 48k stars) and Research Biomedical Databases (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Kegg Analysis?
davepoon (a GitHub user) maintains it in davepoon/buildwithclaude, which has 3,605 GitHub stars. The repository holds 246 skills in this directory. The repository was last updated on October 9, 2026.
Source: davepoon/buildwithclaude on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.