MRMhub-QUANT is a programmatic library for tailored, reproducible post-processing and quality-control of targeted metabolomics and lipidomics analyses. It works with MRMhub-INTEGRATOR peak integration results, or feature intensity data from other sources (CSV, mzTab-M, Skyline). It is the post-processing module of MRMhub and distributed as the R package mrmhub. It features:
- Reproducible pipelines. Script, explore and document, with QC visualisations at every step.
- Flexible workflows. Customisable functions for metabolomics and lipidomics post-processing.
- A single data object. Data, metadata, and processing results live in one shareable object.
Quick Start
- Installation - install and verify your setup
- Getting started with R and Quarto - Setting up R, an editor, and a Quarto project
- Getting started with MRMhub - a first end-to-end analysis on the bundled data
- Try the interactive workflow builder - generate a runnable Quarto notebook
- Run the demo ↗ - a bundled, runnable demo project with data
Example Workflows
- Example: targeted lipidomics - a full lipidomics workflow
- Example: external calibration - a quantitative assay with calibration curves
- Browse real analyses ↗ - annotated, end-to-end reports from large-scale studies
Installing and Updating
Make sure to use a fresh R session without loaded packages (restart RStudio/Positron first).
Read the Installation guide before installing.
# mrmhub from the MRMhub R-universe repository, dependencies from CRAN
install.packages("mrmhub",
repos = c("https://slinghub.r-universe.dev",
"https://cloud.r-project.org"))
library(mrmhub)The same command installs later updates. Alternative methods using pak or remotes are described in the guide.
Contributing
Bug reports and feature requests are welcome via GitHub issues. The project follows the Contributor Code of Conduct.
License
Dual-licensed - non-commercial under GNU AGPLv3. For commercial use contact Jonathan Tan (jonathan_tan@nus.edu.sg).