MRMhub-QUANT

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). Please read the Installation guide first for full instructions and troubleshooting.

if (!require("pak")) install.packages("pak")
pak::pak("SLINGhub/MRMhub")
library(mrmhub)

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).