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Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with --group1-prefix / --group2-prefix column matching, BH-FDR…
Install Metabolomics Statistics
$ npx skills add TianGzlab/OmicsClaw --skill metabolomics-statistics -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw metabolomics-statistics --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/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/metabolomics/metabolomics-statistics .claude/skills/metabolomics-statistics && 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 "metabolomics-statistics" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statistics into .claude/skills/metabolomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-statistics", 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/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statisticsType 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 TianGzlab/OmicsClaw --skill metabolomics-statistics -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw metabolomics-statistics --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/metabolomics/metabolomics-statistics .agents/skills/metabolomics-statistics && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "metabolomics-statistics" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statistics into .agents/skills/metabolomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-statistics", 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 TianGzlab/OmicsClaw --skill metabolomics-statistics -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw metabolomics-statistics --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/metabolomics/metabolomics-statistics .cursor/skills/metabolomics-statistics && 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 "metabolomics-statistics" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statistics into .cursor/skills/metabolomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-statistics", 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/TianGzlab/OmicsClaw.git --path skills/metabolomics/metabolomics-statistics--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 TianGzlab/OmicsClaw --skill metabolomics-statistics -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw metabolomics-statistics --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/metabolomics/metabolomics-statistics .gemini/skills/metabolomics-statistics && 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 "metabolomics-statistics" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statistics into .gemini/skills/metabolomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-statistics", 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 TianGzlab/OmicsClaw metabolomics-statisticsInstalls 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 TianGzlab/OmicsClaw --skill metabolomics-statistics -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/metabolomics/metabolomics-statistics .github/skills/metabolomics-statistics && 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 "metabolomics-statistics" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statistics into .github/skills/metabolomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-statistics", 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 TianGzlab/OmicsClaw --skill metabolomics-statistics -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TianGzlab/OmicsClaw metabolomics-statistics --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/metabolomics/metabolomics-statistics .opencode/skills/metabolomics-statistics && 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 "metabolomics-statistics" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/metabolomics/metabolomics-statistics into .opencode/skills/metabolomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "metabolomics-statistics", 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-statistics- GitHub stars
- 161
- Token cost
- ~991 tokens
- SKILL.md length
- 332 words
- Files
- 8 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with --group1-prefix / --group2-prefix column matching, BH-FDR…
- 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
What it does
Metabolomics Statistics is an agent skill from TianGzlab/OmicsClaw. Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with --group1-prefix / --group2-prefix column matching, BH-FDR adjusted. Skip when working with raw spectra (use metabolomics-xcms-preprocessing); two-group DE with default ctrl / treat prefixes (use metabolomics-de).
Its SKILL.md is about 990 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 `metabolomics_statistics.py`).
It sits in Data & Analytics, covering Statistics. 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
Example prompts
- “/metabolomics-statistics”
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 Statistics loads about 991 tokens when it runs, and up to ~1.3k if it reads all its reference files. Until then it costs about 95 tokens; SKILL.md has 332 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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 332 words, ~991 tokens.
Download SKILL.mdSave it as
.claude/skills/metabolomics-statistics/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.- name
- metabolomics-statistics
- description
- Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with `--group1-prefix` / `--group2-prefix` column matching, BH-FDR adjusted. Skip when working with raw spectra (use metabolomics-xcms-preprocessing); two-group DE with default `ctrl` / `treat` prefixes (use metabolomics-de).
- trigger
- metabolomics statistics, multivariate, PCA, clustering
- tags
- metabolomics, statistics, ttest, wilcoxon, anova, kruskal, bh-fdr
metabolomics-statistics
When to use
Test two explicit sample groups using Welch, ranksums, ANOVA or Kruskal. Use metabolomics-de for the ctrl/treat contrast and PCA CLI.
Use from a step
import pandas as pd
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("metabolomics-statistics")
data = read_input('features.csv', reader=lambda path: pd.read_csv(path, index_col=0))
result = library.test_groups(data, group1_prefix='ctrl', group2_prefix='treat')
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 -->test_groups(data, *, method='ttest', alpha=0.05, group1_prefix=None, group2_prefix=None, group1_cols=None, group2_cols=None)
Return two-group test statistics and BH-adjusted p values.
:param data: Numeric feature-by-sample DataFrame with feature IDs as its index. :param method: CLI default ttest; wilcoxon (ranksums), anova or kruskal also work. :param alpha: CLI default .05; diagnostic significance threshold. :param group1_prefix: CLI default None; prefix selecting the reference samples. :param group2_prefix: CLI default None; prefix selecting the comparison samples. :param group1_cols: Explicit reference columns; supply together with group2_cols. :param group2_cols: Explicit comparison columns; overrides prefix selection. :returns: A new DataFrame with grouping and significance diagnostics. :raises ValueError: A group is empty, overlaps another or is only partly specified.
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.
volcano_figure(data)
Plot group2/group1 log2 fold change against BH-adjusted significance.
:param data: Results from test_groups. :returns: A matplotlib Figure. :raises KeyError: log2fc or fdr is absent.
<!-- api:end -->Methods and parameters
The wilcoxon label calls scipy.stats.ranksums, not paired Wilcoxon or Mann-Whitney U. ANOVA and Kruskal accept exactly two groups here. BH FDR covers every returned feature.
Gotchas
test_groupsfalls back to midpoint grouping with a warning when both prefixes are not supplied; run_info records the columns.tables/significant.csvuses fdr < alpha. log2fc is group2/group1.
Inputs and outputs
CSV input; tables/statistics.csv, report.md and result.json. The CLI also writes tables/significant.csv. The CLI writes reproducibility/commands.sh.
The function library returns objects; the CLI and step own file writes.
CLI
python skills/metabolomics/metabolomics-statistics/metabolomics_statistics.py --demo --output /tmp/metabolomics_statisticsSee also
Dependencies
numpy, pandas, scipy, matplotlib
© TianGzlab, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 7 other files (references) in skills/metabolomics/metabolomics-statistics of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- examples/example_step.py
- metabolomics_statistics.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 Statistics 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 |
|---|---|---|---|---|---|---|
| Metabolomics Statistics this skillTianGzlab/OmicsClaw | 161 | — | ~991 | Automated safety check: Pass | Apache-2.0 | |
| Sandbox Benchvercel/next.js | 143k | — | ~4.1k | Automated safety check: Pass | MIT | |
| Statistical Analysisspacering-net/codeg | 3.9k | 3 repos | ~5k | Automated safety check: Pass | MIT | |
| StatsmodelszLanqing/codex-claude-academic-skills | 4.7k | 15 repos | ~4.9k | Automated safety check: Pass | BSD-3-Clause | |
| AI Daily DigestvigorX777/ai-daily-digest | 1.6k | — | ~1.3k | Automated safety check: Pass | None | |
| Statistical Powerspacering-net/codeg | 3.9k | 1 repos | ~3.6k | Automated safety check: Notes | MIT |
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Related
Categories
Questions about Metabolomics Statistics
What does Metabolomics Statistics do?
Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with --group1-prefix / --group2-prefix column matching, BH-FDR…. Metabolomics Statistics is an agent skill from TianGzlab/OmicsClaw. Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with --group1-prefix / --group2-prefix column matching, BH-FDR adjusted.
When should I use Metabolomics Statistics?
Metabolomics Statistics fits situations like: tasks that involve Statistics.
How do I install Metabolomics Statistics in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill metabolomics-statistics -a claude-code`. Or copy the skill folder (skills/metabolomics/metabolomics-statistics in TianGzlab/OmicsClaw) into .claude/skills/metabolomics-statistics in your project. Claude Code loads it when a task matches its description.
How do I install Metabolomics Statistics in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill metabolomics-statistics -a codex`. Or copy the skill folder (skills/metabolomics/metabolomics-statistics in TianGzlab/OmicsClaw) into .agents/skills/metabolomics-statistics in your project. Codex loads it when a task matches its description.
Can I use Metabolomics Statistics 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-statistics -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-statistics, .gemini/skills/metabolomics-statistics, .github/skills/metabolomics-statistics and .opencode/skills/metabolomics-statistics in your project.
What does Metabolomics Statistics need to run?
Going by SKILL.md and its folder, Metabolomics Statistics needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Metabolomics Statistics 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 Statistics 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 Statistics use?
Metabolomics Statistics 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 Statistics use?
About 991 tokens (SKILL.md is roughly 4k 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 316 tokens, read only when the agent opens those files.
What are the alternatives to Metabolomics Statistics?
Skills that share tags, products or a category with Metabolomics Statistics: Sandbox Bench (vercel/next.js, 143k stars), Statistical Analysis (spacering-net/codeg, 3.9k stars), Statsmodels (zLanqing/codex-claude-academic-skills, 4.7k stars) and AI Daily Digest (vigorX777/ai-daily-digest, 1.6k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Metabolomics Statistics?
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.