bio-metabolomics-msdial-preprocessing
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-msdial-preprocessing --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.
## Version Compatibility Reference examples tested with: numpy 1.26+, pandas 2.2+, scanpy 1.10+, xcms 4.0+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # MS-DIAL Preprocessing **"Process my LC-MS data with MS-DIAL"** → Detect chromatographic peaks, align across samples, annotate metabolites, and export a feature table for statistical analysis. - CLI: MS-DIAL GUI or console mode for peak picking and alignment ## MS-DIAL GUI Workflow MS-DIAL provides a user-friendly GUI for complete metabolomics preprocessing: 1. **Project Setup** - Create new project, select data type 2. **Data Import** - Load mzML/ABF files 3. **Peak Detection** - Automatic peak picking 4. **Alignment** - Cross-sample alignment 5. **Gap Filling** - Fill missing values 6. **Annotation** - Database matching 7. *
- Version Compatibility
- MS-DIAL GUI Workflow
- Export MS-DIAL Results to R
- Filter MS-DIAL Results
- MS-DIAL Data to XCMS-Like Format
- MS-DIAL Batch Processing (Console Mode)
- Parameter File Example
- Python Processing of MS-DIAL Output
- MS-DIAL Annotation Levels
- Compare MS-DIAL vs XCMS Results
- Export for MetaboAnalyst
- Normalization Options
- Related Skills
MS-DIAL console application for batch processing Available on Windows Create parameter file (msdial_param.txt) See MS-DIAL documentation for all parameters Run MS-DIAL console MsdialConsoleApp.exe lcmsdda -i input_folder -o output_folder -m msdial_param.txt
What does the bio-metabolomics-msdial-preprocessing skill do?
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-msdial-preprocessing --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.