matchms
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill matchms --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Matchms ## Overview Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various formats, standardize metadata, filter peaks, calculate spectral similarities, and build reproducible analytical workflows. ## Core Capabilities ### 1. Importing and Exporting Mass Spectrometry Data Load spectra from multiple file formats and export processed data: ```python from matchms.importing import load_from_mgf, load_from_mzml, load_from_msp, load_from_json from matchms.exporting import save_as_mgf, save_as_msp, save_as_json # Import spectra spectra = list(load_from_mgf("spectra.mgf")) spectra = list(load_from_mzml("data.mzML")) spectra = list(load_from_msp("library.msp")) # Export processed spectra save_as_mgf(spectra, "output.mgf") save_as_json(spectra, "output.json") ``` **Supported formats:** - mzML and mzXML (raw mass spectrometry formats) - MGF (Mascot Generic Format) - MSP (spectral library format) - JSON (GNPS-compatible) - metabolomics-USI references - Pickle (Python serialization) For detailed importing/exporting documentation, consult `references/importing_exporting.md`. ### 2. Spectrum Filtering and Processing Apply compreh
- Overview
- Core Capabilities
- 1. Importing and Exporting Mass Spectrometry Data
- 2. Spectrum Filtering and Processing
- 3. Calculating Spectral Similarities
- 4. Building Processing Pipelines
- 5. Working with Spectrum Objects
- 6. Metadata Management
- Common Workflows
- Installation
- Reference Documentation
uv pip install matchms uv pip install matchms[chemistry]
What does the matchms skill do?
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill matchms --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.