Bio Metabolomics Xcms Preprocessing
GPTomics/bioSkills
Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time…
Agent skill
Bio Metabolomics Xcms Preprocessing
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
No licenceAuto-check passed
Install Bio Metabolomics Xcms Preprocessing
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-metabolomics-xcms-preprocessing --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-metabolomics-xcms-preprocessing .claude/skills/bio-metabolomics-xcms-preprocessing && 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 "bio-metabolomics-xcms-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessing into .claude/skills/bio-metabolomics-xcms-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-metabolomics-xcms-preprocessing", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessingType 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-metabolomics-xcms-preprocessing --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-metabolomics-xcms-preprocessing .agents/skills/bio-metabolomics-xcms-preprocessing && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-metabolomics-xcms-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessing into .agents/skills/bio-metabolomics-xcms-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-metabolomics-xcms-preprocessing", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-metabolomics-xcms-preprocessing --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-metabolomics-xcms-preprocessing .cursor/skills/bio-metabolomics-xcms-preprocessing && 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 "bio-metabolomics-xcms-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessing into .cursor/skills/bio-metabolomics-xcms-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-metabolomics-xcms-preprocessing", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-metabolomics-xcms-preprocessing--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-metabolomics-xcms-preprocessing --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-metabolomics-xcms-preprocessing .gemini/skills/bio-metabolomics-xcms-preprocessing && 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 "bio-metabolomics-xcms-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessing into .gemini/skills/bio-metabolomics-xcms-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-metabolomics-xcms-preprocessing", 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 FreedomIntelligence/OpenClaw-Medical-Skills bio-metabolomics-xcms-preprocessingInstalls 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-metabolomics-xcms-preprocessing .github/skills/bio-metabolomics-xcms-preprocessing && 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 "bio-metabolomics-xcms-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessing into .github/skills/bio-metabolomics-xcms-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-metabolomics-xcms-preprocessing", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-metabolomics-xcms-preprocessing --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-metabolomics-xcms-preprocessing .opencode/skills/bio-metabolomics-xcms-preprocessing && 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 "bio-metabolomics-xcms-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-xcms-preprocessing into .opencode/skills/bio-metabolomics-xcms-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-metabolomics-xcms-preprocessing", 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
bio-metabolomics-xcms-preprocessing- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2k tokens
- SKILL.md length
- 453 words
- Files
- 3
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
- Processing raw LC-MS data into a feature table for untargeted metabolomics
- SKILL.md covers Version Compatibility, Load Raw Data, Define Sample Groups and Peak Detection (Centroided), plus 9 more sections
- Runs R scripts from its folder
What it does
Bio Metabolomics Xcms Preprocessing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Processing raw LC-MS data into a feature table for untargeted metabolomics
Example prompts
- “/bio-metabolomics-xcms-preprocessing”
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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 (R), which the agent can run.
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
Bio Metabolomics Xcms Preprocessing loads about 2k tokens when it runs. Until then it costs about 67 tokens; SKILL.md has 453 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
Without a licence we can't republish the file, so here is its outline and opening line. It has 453 words (~1,998 tokens).
“Reference examples tested with: MSnbase 2.28+, scanpy 1.10+, xcms 4.0+”
- name
- bio-metabolomics-xcms-preprocessing
- tool_type
- r
- primary_tool
- xcms
Files
SKILL.md and 2 other files in skills/bio-metabolomics-xcms-preprocessing of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/xcms_workflow.R
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Bio Metabolomics Xcms Preprocessing 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 |
|---|---|---|---|---|---|---|
| Bio Metabolomics Xcms Preprocessing this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| Bio Metabolomics Xcms PreprocessingGPTomics/bioSkills | 1.2k | 1 repos | ~4.3k | Automated safety check: Pass | MIT | |
| Bio Metabolomics Msdial PreprocessingGPTomics/bioSkills | 1.2k | 1 repos | ~4k | Automated safety check: Pass | MIT | |
| Bio Metabolomics Msdial Preprocessingmajiayu000/claude-skill-registry | 666 | 2 repos | ~2.1k | Automated safety check: Pass | MIT | |
| Metabolomics Xcms PreprocessingTianGzlab/OmicsClaw | 161 | — | ~566 | Automated safety check: Pass | Apache-2.0 | |
| Bio Workflows Metabolomics PipelineGPTomics/bioSkills | 1.2k | 1 repos | ~4.8k | Automated safety check: Pass | MIT |
Similar skills
Bio Metabolomics Msdial Preprocessing
GPTomics/bioSkills
Runs the MS-DIAL preprocessing workflow (peak picking, MS2Dec spectral deconvolution, alignment, gap-filling) and imports the alignment-result table into R or Python with honest filtering.
Bio Metabolomics Msdial Preprocessing
majiayu000/claude-skill-registry
MS-DIAL-based metabolomics preprocessing as alternative to XCMS.
Metabolomics Xcms Preprocessing
TianGzlab/OmicsClaw
Load when exercising the CLI and replay pipeline with a synthetic LC-MS peak table.
Bio Workflows Metabolomics Pipeline
GPTomics/bioSkills
Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics…
Bio Metabolomics Pathway Mapping
GPTomics/bioSkills
Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with…
More from FreedomIntelligence/OpenClaw-Medical-Skills
All 170 skills in this repoDifferentiation Schemes
FreedomIntelligence/OpenClaw-Medical-Skills
Select and apply numerical differentiation schemes for PDE/ODE discretization.
Medical Research Toolkit
FreedomIntelligence/OpenClaw-Medical-Skills
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
Mesh Generation
FreedomIntelligence/OpenClaw-Medical-Skills
Plan and evaluate mesh generation for numerical simulations.
Numerical Integration
FreedomIntelligence/OpenClaw-Medical-Skills
Select and configure time integration methods for ODE/PDE simulations.
Ontology Explorer
FreedomIntelligence/OpenClaw-Medical-Skills
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy).
Ontology Mapper
FreedomIntelligence/OpenClaw-Medical-Skills
Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties.
Questions about Bio Metabolomics Xcms Preprocessing
What does Bio Metabolomics Xcms Preprocessing do?
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bio Metabolomics Xcms Preprocessing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. XCMS3 workflow for LC-MS/MS metabolomics preprocessing.
When should I use Bio Metabolomics Xcms Preprocessing?
Bio Metabolomics Xcms Preprocessing fits situations like: processing raw LC-MS data into a feature table for untargeted metabolomics.
How do I install Bio Metabolomics Xcms Preprocessing in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a claude-code`. Or copy the skill folder (skills/bio-metabolomics-xcms-preprocessing in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-metabolomics-xcms-preprocessing in your project. Claude Code loads it when a task matches its description.
How do I install Bio Metabolomics Xcms Preprocessing in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a codex`. Or copy the skill folder (skills/bio-metabolomics-xcms-preprocessing in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-metabolomics-xcms-preprocessing in your project. Codex loads it when a task matches its description.
Can I use Bio Metabolomics Xcms Preprocessing 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-xcms-preprocessing -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-metabolomics-xcms-preprocessing, .gemini/skills/bio-metabolomics-xcms-preprocessing, .github/skills/bio-metabolomics-xcms-preprocessing and .opencode/skills/bio-metabolomics-xcms-preprocessing in your project.
What does Bio Metabolomics Xcms Preprocessing need to run?
Going by SKILL.md and its folder, Bio Metabolomics Xcms Preprocessing needs R for the scripts in its folder.
Does Bio Metabolomics Xcms Preprocessing 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 Bio Metabolomics Xcms Preprocessing 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 Bio Metabolomics Xcms Preprocessing use?
No licence was found for Bio Metabolomics Xcms Preprocessing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Metabolomics Xcms Preprocessing use?
About 2k tokens (SKILL.md is roughly 8k 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 Bio Metabolomics Xcms Preprocessing?
Skills that share tags, products or a category with Bio Metabolomics Xcms Preprocessing: Bio Metabolomics Xcms Preprocessing (GPTomics/bioSkills, 1.2k stars), Bio Metabolomics Msdial Preprocessing (GPTomics/bioSkills, 1.2k stars), Bio Metabolomics Msdial Preprocessing (majiayu000/claude-skill-registry, 666 stars) and Metabolomics Xcms Preprocessing (TianGzlab/OmicsClaw, 161 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Metabolomics Xcms Preprocessing?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.