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metabolomics-pathway-enrichment

metabolomics-pathway-enrichment is a skill for Claude Code, Codex from TianGzlab/OmicsClaw. It costs 84 tokens per session (1,295 once invoked), scanned A, original, Apache-2.0.

A demo metabolomics analysis that tests whether a list of metabolites is over-represented in predefined biological pathways. A pathway is a group of related chemical reactions in a cell.

In plain words
What is it for?
Use it for Fisher's exact test and false-discovery-rate analysis of metabolite lists against the included demo pathways.
Why use it?
It provides a way to connect a metabolite list with possible biological processes instead of reviewing each metabolite separately. Its pathway database is limited to a built-in nine-pathway demo set.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 160repo 1mo ago A scan SkillSpector: warn 84 tokens original Apache-2.0

Good fit Use it for Fisher's exact test and false-discovery-rate analysis of metabolite lists against the included demo pathways.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment
View source ↗ TianGzlab/OmicsClaw tiangzlab.github.io
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add TianGzlab/OmicsClaw --skill metabolomics-pathway-enrichment
Clone the repo
git clone --depth 1 https://github.com/TianGzlab/OmicsClaw

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for metabolomics-pathway-enrichment

README.md
[![agentmods](https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment/github.svg)](https://agentmods.dev/skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment)
Your own site
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for metabolomics-pathway-enrichment

Your own site · 80×15
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/metabolomics-pathway-enrichment.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 84 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,295 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 1 finding, up to high

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • high Rogue Agent · line 3
    Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.
    Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00084 $0.01295
Opus 5 $0.00042 $0.00647
Sonnet 5 $0.00017 $0.00259
Haiku 4.5 $0.00008 $0.00129

Measured 7d ago against content hash 47cdb9f8ec95, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

metabolomics-pathway-enrichment scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (met_pathway.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/metabolomics/metabolomics-pathway-enrichment/SKILL.md · 94 lines

How it starts

The opening of the file, as written. The whole thing — 94 lines — stays where its author put it; the contents beside it link to each section on GitHub.

metabolomics-pathway-enrichment

When to use

The user has a CSV listing metabolites of interest (e.g. significant features from metabolomics-de or metabolomics-statistics, joined with their HMDB / KEGG names) and wants over-representation enrichment via Fisher's exact test, with BH-adjusted FDR.

This is a demo-only enrichment. The pathway database is the hard-coded 9-pathway DEMO_METABOLIC_PATHWAYS dict at met_pathway.py:45-104 (e.g. glycolysis, TCA cycle, amino-acid metabolism). There is NO CLI flag to load real KEGG / Reactome / SMPDB. For production metabolomics enrichment, route to external tools (MetaboAnalystR, mummichog, FELLA) or send the metabolite list through bulkrna-enrichment after gene-mapping.

Inputs & Outputs

Inputs

  • File types: .csv
  • Accepts artifact metabolomics.differential_results (csv)

Outputs

  • tables/pathway_enrichment.csv
  • report.md
  • result.json

Flow

  1. Load CSV (--input <metabolites.csv>) or generate a demo at output_dir/<demo>.csv (met_pathway.py:300).
  2. Pick the metabolite-list column: metabolite if present, otherwise the first column (met_pathway.py:307).
  3. For each pathway in DEMO_METABOLIC_PATHWAYS (met_pathway.py:45), run Fisher's exact test (hypergeometric) (met_pathway.py:132-200); apply BH FDR adjustment (:198).
  4. Write tables/pathway_enrichment.csv (met_pathway.py:314) + report.md + result.json.

Gotchas

  • Pathway database is HARD-CODED 9 demo pathways. met_pathway.py:45-104 defines DEMO_METABOLIC_PATHWAYS (e.g. glycolysis, TCA cycle, urea cycle). The n_pathways_tested = 9 in result.json (:320) is constant. For real enrichment, use MetaboAnalystR / mummichog / FELLA externally.
  • --method mummichog and --method fella are RECORDED-ONLY. met_pathway.py:293 accepts choices=["ora", "mummichog", "fella"] but pathway_enrichment (:132-200) ignores the method parameter — only ORA (Fisher's exact + BH FDR) is implemented. Calling with --method mummichog produces ORA results plus a misleading method=mummichog label in result.json.
  • Metabolite-name matching is CASE-INSENSITIVE substring. met_pathway.py:165 lower-cases both query and pathway-member names. glucose, Glucose, D-Glucose all match a pathway entry D-Glucose — but Hexose will NOT.
  • Column auto-detection: metabolite first, else first column. met_pathway.py:307 uses met_col = "metabolite" if "metabolite" in df.columns else df.columns[0]. Pre-rename if your CSV has multiple ID columns (name, hmdb_id, kegg).
  • --input REQUIRED unless --demo. met_pathway.py:303 raises ValueError("--input required when not using --demo").

Read the full file on GitHub · 94 lines

Files

What ships with it

5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 7d ago First seen · 94 lines · 84 tokens per session scan A 47cdb9f8ec95

Subscribe to this mod's changes

metabolomics-pathway-enrichment is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 84 tokens to every session and 1,295 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

ORAScientificSingle-Cellbioinformaticsdemoenrichmentfisherknowledge-graphllm-agentmetabolomicsmulti-agentsmulti-omicspathway
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