BI
Data & Repro
bio-metabolomics-lipidomics
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSear…
FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-metabolomics-msdial-preprocessing
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-msdial-preprocessing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: MS-DIAL GUI or console mode for peak picking and alignment.
- 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.
- msdial_data <- read.csv('msdial_alignment_result.csv', check.names = FALSE).
Source Doc
Excerpt From SKILL.md
MS-DIAL GUI Workflow
MS-DIAL provides a user-friendly GUI for complete metabolomics preprocessing:
- Project Setup - Create new project, select data type
- Data Import - Load mzML/ABF files
- Peak Detection - Automatic peak picking
- Alignment - Cross-sample alignment
- Gap Filling - Fill missing values
- Annotation - Database matching
- Export - Export for downstream analysis
Identify sample columns (contain "Area" or sample names)
sample_cols <- grep('Area$|^Sample', colnames(msdial_data), value = TRUE) meta_cols <- setdiff(colnames(msdial_data), sample_cols)
Extract feature metadata
feature_info <- msdial_data[, meta_cols]
Use cases
- Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- xcms-preprocessing - Alternative preprocessing with XCMS
- metabolite-annotation - Additional annotation methods
- normalization-qc - Detailed normalization approaches
- lipidomics - Lipid-specific MS-DIAL workflows
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