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 majiayu000/claude-skill-registry --skill 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.
# MS-DIAL Preprocessing ## 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. **Export** - Export for downstream analysis ## Export MS-DIAL Results to R ```r library(tidyverse) # Load MS-DIAL alignment result msdial_data <- read.csv('msdial_alignment_result.csv', check.names = FALSE) # Typical columns from MS-DIAL export # Alignment ID, Average Rt(min), Average Mz, Metabolite name, Adduct type, # Fill %, MS/MS assigned, Reference RT, Reference m/z, Formula, Ontology, # INCHIKEY, SMILES, Annotation tag (Level), Comment, [Sample columns...] # 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] # Extract intensity matrix intensity_matrix <- as.matrix(msdial_data[, sample
- 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 majiayu000/claude-skill-registry --skill 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 majiayu000/claude-skill-registry, a repository with 534 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.