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tidyXCMS

Tidy interface for XCMS metabolomics data processing

Overview

tidyXCMS provides a modern, tidy interface for working with XCMS metabolomics data, making it easier to integrate XCMS workflows with the tidyverse ecosystem.

Installation 

# Install from GitHub
# devtools::install_github("stanstrup/tidyXCMS")

Usage 

library(tidyXCMS)
library(xcms)

# Load preprocessed XCMS data
xdata <- loadXcmsData("xmse")

# Create long-format peak table
peak_table <- tidy_peaklist(xdata)

# Result: one row per feature per sample
# Includes peak intensities, m/z, RT, and sample metadata
head(peak_table)

Optional annotations:

  • CAMERA: Group features by retention time, correlation across samples or EIC similarity. Add isotope, adduct, and pseudo-spectra annotations
  • MsFeatures: Group features by retention time and correlation across samples.

See the vignette for detailed examples.

Development

This package uses:

  • Semantic versioning via semantic-release
  • Automated documentation via pkgdown
  • Continuous integration via GitHub Actions

License

MIT License