Agent skill

Metabolomics De

Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat).

Apache-2.0Auto-check passedData & Analytics

Install Metabolomics De

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw metabolomics-de --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/metabolomics/metabolomics-de .claude/skills/metabolomics-de && rm -rf skills-src

Use ~/.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/

Paste into Claude Code

Install the "metabolomics-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de into .claude/skills/metabolomics-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-de", 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

$skill-installer install https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de

Type 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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw metabolomics-de --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/metabolomics/metabolomics-de .agents/skills/metabolomics-de && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "metabolomics-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de into .agents/skills/metabolomics-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-de", 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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw metabolomics-de --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/metabolomics/metabolomics-de .cursor/skills/metabolomics-de && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "metabolomics-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de into .cursor/skills/metabolomics-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-de", 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

$ gemini skills install https://github.com/TianGzlab/OmicsClaw.git --path skills/metabolomics/metabolomics-de

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw metabolomics-de --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/metabolomics/metabolomics-de .gemini/skills/metabolomics-de && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "metabolomics-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de into .gemini/skills/metabolomics-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-de", 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.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw metabolomics-de

Installs 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).

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/metabolomics/metabolomics-de .github/skills/metabolomics-de && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "metabolomics-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de into .github/skills/metabolomics-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-de", 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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw metabolomics-de --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/metabolomics/metabolomics-de .opencode/skills/metabolomics-de && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "metabolomics-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-de into .opencode/skills/metabolomics-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-de", 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: metabolomics-de
GitHub stars: 161
Token cost: ~983 tokens
SKILL.md length: 353 words
Files: 8 (incl. references)
Skills in repo: 88
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat).

Tasks that involve Statistics
SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
Runs Python scripts from its folder; calls python
Tasks that involve CSV and tabular files

What it does

Metabolomics De is an agent skill from TianGzlab/OmicsClaw. Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat). Skip when needing tunable test backends (use metabolomics-statistics); raw spectra.

Its SKILL.md is about 980 tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files, including reference files (for example `_api.py`, `examples/example_step.py` and `met_diff.py`).

It sits in Data & Analytics, covering Statistics and CSV and tabular files. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Statistics
Tasks that involve CSV and tabular files

Example prompts

“/metabolomics-de”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 90a3bec. 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 (Python), which the agent can run.
Shell commands in SKILL.md call:
- 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

Metabolomics De loads about 983 tokens when it runs, and up to ~1.3k if it reads all its reference files. Until then it costs about 69 tokens; SKILL.md has 353 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~69
When it runs · the whole SKILL.md, loaded when a task matches: ~983
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.3k

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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 353 words, ~983 tokens.

Download SKILL.mdSave it as .claude/skills/metabolomics-de/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.

name: metabolomics-de
description: Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using `--group-a-prefix` / `--group-b-prefix` (default `ctrl` / `treat`). Skip when needing tunable test backends (use metabolomics-statistics); raw spectra.
trigger: metabolomics differential, PLS-DA, volcano plot, biomarker, OPLS-DA
tags: metabolomics, de, ttest, pca, bh-fdr, biomarker

metabolomics-de

When to use

Run Welch tests and treatment/control fold changes using ctrl/treat sample prefixes. Use metabolomics-statistics for another test backend.

Use from a step

python

import pandas as pd
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("metabolomics-de")
data = read_input('features.csv', reader=pd.read_csv)
result = library.differential_expression(data)
write_output(result, 'tables/result.csv')

examples/example_step.py runs a seeded synthetic example through the step runner and writes a table and Figure. Computations return new DataFrames, leave the input unchanged and expose diagnostics through run_info(result). Plotting functions write no files.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->

`differential_expression(data, *, group_a_prefix='ctrl', group_b_prefix='treat')`

Return Welch tests, treatment/control log2 fold changes and BH FDR.

:param data: Feature table whose first column identifies features; other columns contain intensities. :param group_a_prefix: CLI default ctrl; prefix selecting control samples. :param group_b_prefix: CLI default treat; prefix selecting treatment samples. :returns: A new differential table with group sizes in attrs['run_info']. :raises ValueError: A group is absent or groups overlap.

`run_info(data, *, keep=True)`

Read diagnostics attached to a returned table.

:param data: DataFrame returned by this library. :param keep: Default True; use False in the CLI to remove diagnostics. :returns: An independent dictionary describing the run. :raises ValueError: The table carries no run_info.

`pca_figure(data, *, group_a_prefix='ctrl', group_b_prefix='treat', random_state=0)`

Plot sample PCA from untransformed intensities; NaNs become zero.

:param data: Feature table with the same sample columns as differential_expression. :param group_a_prefix: CLI default ctrl; control prefix. :param group_b_prefix: CLI default treat; treatment prefix. :param random_state: Default 0; seed forwarded to sklearn PCA. :returns: A matplotlib Figure with sample labels and explained variance axes. :raises ImportError: Install scikit-learn with install_skill_deps if unavailable. :raises ValueError: Groups are absent, overlap or the matrix is invalid.

<!-- api:end -->

Show full SKILL.md (111 more words)Show less

Methods and parameters

Welch tests use raw supplied intensities, with BH FDR and a fixed CLI significance threshold of 0.05. PCA uses untransformed intensities and converts NaNs to zero.

Gotchas

differential_expression treats the first column as feature IDs. Both groups must be nonempty and disjoint. tables/significant_features.csv uses fdr < 0.05. The CLI logs optional PCA failures.

Inputs and outputs

CSV input; tables/differential_features.csv, report.md and result.json. The CLI also writes tables/significant_features.csv and, when PCA succeeds, figures/pca_scores.png. Demo mode also writes its synthetic input CSV at the output root. The function library returns objects; the CLI and step own file writes.

CLI

bash

python skills/metabolomics/metabolomics-de/met_diff.py --demo --output /tmp/metabolomics_de

Dependencies

numpy, pandas, scipy, scikit-learn, matplotlib

Files

SKILL.md and 7 other files (references) in skills/metabolomics/metabolomics-de of TianGzlab/OmicsClaw.

SKILL.md
_api.py
examples/example_step.py
met_diff.py
references/methodology.md
references/output_contract.md
references/parameters.md
tests/test_api.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Metabolomics De 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.

Metabolomics De compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Metabolomics De this skillTianGzlab/OmicsClaw	161	—	~983	Automated safety check: Pass	Apache-2.0	3 days ago
Analysis Graphingclshortfuse/renodx	4.5k	—	~1.1k	Automated safety check: Pass	MIT	yesterday
Eqtl Catalogue Region FetchClawBio/ClawBio	1.2k	1 repos	~4.7k	Automated safety check: Pass	MIT	yesterday
CSV Data Analysis5zjk5/prompt-engineering	127	—	~2.6k	Automated safety check: Pass	None	25 days ago
Gwas Catalog Region FetchClawBio/ClawBio	1.2k	1 repos	~3.5k	Automated safety check: Pass	MIT	yesterday
Data Analysisfastclaw-ai/fastclaw	1.4k	—	~410	Automated safety check: Pass	Custom licence	yesterday

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Questions about Metabolomics De

What does Metabolomics De do?

Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat). Metabolomics De is an agent skill from TianGzlab/OmicsClaw. Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat).

When should I use Metabolomics De?

Metabolomics De fits situations like: tasks that involve Statistics; tasks that involve CSV and tabular files.

How do I install Metabolomics De in Claude Code?

Run `npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a claude-code`. Or copy the skill folder (skills/metabolomics/metabolomics-de in TianGzlab/OmicsClaw) into .claude/skills/metabolomics-de in your project. Claude Code loads it when a task matches its description.

How do I install Metabolomics De in Codex?

Run `npx skills add TianGzlab/OmicsClaw --skill metabolomics-de -a codex`. Or copy the skill folder (skills/metabolomics/metabolomics-de in TianGzlab/OmicsClaw) into .agents/skills/metabolomics-de in your project. Codex loads it when a task matches its description.

Can I use Metabolomics De 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 TianGzlab/OmicsClaw --skill metabolomics-de -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/metabolomics-de, .gemini/skills/metabolomics-de, .github/skills/metabolomics-de and .opencode/skills/metabolomics-de in your project.

What does Metabolomics De need to run?

Going by SKILL.md and its folder, Metabolomics De needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Metabolomics De 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 Metabolomics De 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 Metabolomics De use?

Metabolomics De is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Metabolomics De use?

About 983 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. Its references folder adds about 327 tokens, read only when the agent opens those files.

What are the alternatives to Metabolomics De?

Skills that share tags, products or a category with Metabolomics De: Analysis Graphing (clshortfuse/renodx, 4.5k stars), Eqtl Catalogue Region Fetch (ClawBio/ClawBio, 1.2k stars), CSV Data Analysis (5zjk5/prompt-engineering, 127 stars) and Gwas Catalog Region Fetch (ClawBio/ClawBio, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Metabolomics De?

TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 2026.

Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Metabolomics De

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

metabolomics-de

When to use

Use from a step

API

differential_expression(data, *, group_a_prefix='ctrl', group_b_prefix='treat')

run_info(data, *, keep=True)

pca_figure(data, *, group_a_prefix='ctrl', group_b_prefix='treat', random_state=0)

Methods and parameters

Gotchas

Inputs and outputs

CLI

See also

Dependencies

Files

Compare with similar skills

Similar skills

More from TianGzlab/OmicsClaw

Related

Questions about Metabolomics De

`differential_expression(data, *, group_a_prefix='ctrl', group_b_prefix='treat')`

`run_info(data, *, keep=True)`

`pca_figure(data, *, group_a_prefix='ctrl', group_b_prefix='treat', random_state=0)`