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metabolomics-de

metabolomics-de is a skill for Claude Code, Codex from TianGzlab/OmicsClaw. It costs 75 tokens per session (1,242 once invoked), scanned A, original, Apache-2.0.

A workflow for comparing two groups of metabolomics measurements, where each row is a measured feature and each column is a sample.

In plain words
What is it for?
Use it on a feature-by-sample CSV with control and treatment column prefixes to run t-tests, calculate log2 fold changes and false-discovery rates, and create a PCA plot.
Why use it?
It identifies features that differ between the groups while correcting for many statistical tests and showing overall sample patterns.

Skill for Claude CodeCodex

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

not rated 160repo +1 1mo ago A scan SkillSpector: warn 75 tokens original Apache-2.0

Good fit Use it on a feature-by-sample CSV with control and treatment column prefixes to run t-tests, calculate log2 fold changes and false-discovery rates, and create a PCA plot.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/tiangzlab/omicsclaw/metabolomics-de
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-de
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-de

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

Your own site · 80×15
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/metabolomics-de"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/metabolomics-de.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 75 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,242 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 $0.00075 $0.01242
Opus 5 $0.00037 $0.00621
Sonnet 5 $0.00015 $0.00248
Haiku 4.5 $0.00007 $0.00124

Measured 9d ago against content hash f3e6288d254a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

metabolomics-de 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 9d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (met_diff.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-de/SKILL.md · 99 lines

How it starts

The opening of the file, as written. The whole thing — 99 lines — stays where its author put it; the contents beside it link to each section on GitHub.

metabolomics-de

When to use

The user has a feature × sample metabolomics CSV with column-name prefixes encoding the two-group design (default ctrl for control, treat for treatment) and wants univariate t-test + log2FC + BH-FDR + a PCA scatter as the canonical "two-group differential analysis" output.

--group-a-prefix and --group-b-prefix are user-tunable (defaults ctrl and treat). For more test backends (Wilcoxon / ANOVA / Kruskal) use metabolomics-statistics.

Inputs & Outputs

Inputs

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

Outputs

  • tables/differential_features.csv
  • tables/significant_features.csv
  • figures/pca_scores.png
  • report.md
  • result.json
  • Produces artifact metabolomics.differential_results as tables/differential_features.csv (csv)

Flow

  1. Load CSV (--input <features.csv>) or generate a demo at output_dir/<demo>.csv (met_diff.py:279).
  2. Filter group columns by prefix (met_diff.py:287-288); raise ValueError("Could not find columns starting with '...' / '...'") at :291 if either group is empty.
  3. Run univariate t-test → pvalue + BH-adjusted fdr + log2FC (met_diff.py:run_univariate).
  4. Filter fdr < 0.05 (HARD-CODED, met_diff.py:303-304) → tables/significant_features.csv.
  5. Best-effort PCA on group_a_cols + group_b_cols → figures/pca_scores.png; failures are logged not raised.
  6. Write tables/differential_features.csv (met_diff.py:301) + tables/significant_features.csv (:305) + report + result.json.

Gotchas

  • Default prefixes are ctrl and treat. met_diff.py:271-272 defaults --group-a-prefix=ctrl and --group-b-prefix=treat. Real input column names like Control_1 / Treated_1 (capital, different word) need explicit --group-a-prefix Control_ --group-b-prefix Treated_.
  • Empty group ⇒ ValueError. met_diff.py:291-294 raises ValueError("Could not find columns starting with '...' / '...'") when either filter returns no columns. Sanity-check the prefixes.
  • FDR threshold is HARD-CODED at 0.05. met_diff.py:303-304 filters de_result[de_result["fdr"] < 0.05] — there is NO --alpha flag. Use metabolomics-statistics if you need a tunable significance threshold.
  • --input REQUIRED unless --demo. met_diff.py:282 raises ValueError("--input required when not using --demo").
  • PCA is best-effort. met_diff.py:309-310 wraps run_pca in try / except — failures (e.g. < 3 samples per group, all-NaN features) only log a warning. The DE table is still written.
  • Test backend is fixed at t-test (Welch). No --method flag here — for backend choice use sibling metabolomics-statistics.

Read the full file on GitHub · 99 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. 9d ago First seen · 99 lines · 75 tokens per session scan A f3e6288d254a

Subscribe to this mod's changes

metabolomics-de is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 75 tokens to every session and 1,242 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 2026-08-30.

ScientificSingle-Cellbh-fdrbioinformaticsbiomarkerdeknowledge-graphllm-agentmetabolomicsmulti-agentsmulti-omicspcattest
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