Code & Software
Open-source R packages, Shiny apps, and bioinformatics tools by Jan Stanstrup for LC-MS metabolomics data preprocessing, compound annotation, retention time prediction, and quality control.
Shiny Apps
Automated quality control for LC-MS metabolomics experiments in real-time — catches drift and instrumental problems early.
Retention time prediction system that maps RTs between LC-MS chromatographic systems, enabling portable compound libraries and cross-system mapping.
Shiny app to decompose a mass to possible molecular formulas.
Mass spectrometry data curation tools.
Local Shiny app for interactive visualization of raw LC-MS data — total ion chromatograms, extracted-ion chromatograms, annotated mass spectra, and 2D/3D maps, built on the RforMassSpectrometry stack.
Peaklist Annotator and Browser.
Waters Logbook. Automatic logbook for Waters RAW files.
R Packages
Metabolomics Data Pre-Processing
Modern, interactive visualization for XCMS metabolomics data using ggplot2 and Plotly.
Converts XCMS output to long-format tidy data, integrating LC-MS processing workflows with the tidyverse. Supports optional feature annotations via CAMERA and MsFeatures.
Unified analytical drift and batch correction for LC-MS metabolomics. Implements multiple published correction methods under a single, consistent API to address within-batch signal drift and between-batch differences while preserving data format.
Unified interface for biological sample-level normalization of metabolomics data. Works with both wide and long format data, with native support for long-format tibbles.
Data massaging utilities for metabolomics: batch correction, NA imputation, normalization, fold change calculation, and dendrogram preparation for heatmaps.
Chemistry & Compound Information
Work-in-progress successor to PredRet. Retention time prediction using monotonically constrained GAMs and the RepoRT database.
R package for retention time prediction.
R functions helpful in working with chemical data.
A collection of common m/z values found in mass spectrometry.
Annotates XCMS peaklists against an in-house MS/MS compound database (built with MScurate). Matches features by m/z, retention time, and spectral similarity score, with built-in RT projection between chromatographic systems via PredRet. Generates PDF annotation reports.
Shiny app for curating compound structures in a CompDb when only CAS numbers are available. Presents candidate structures for manual selection. Primarily for internal use.
Data Import/Export & Databases
Parser for mwtab files from the metabolomicsworkbench.
Package Management
Automatically update R packages from GitHub and GitLab repositories.
Wrappers for Command-line Tools
Obsolete
Click to show/hide obsolete packages
Replacement function for the R function heatmap.2. This function calculates distance after scaling in contrast to heatmap.2.
2014-09-14: Use
2014-09-14: Use
heat.clust in massageR instead together with normal heatmap.2.
Automated processing of chemical standards.
A collection of matlab functions useful for dealing with LC-MS metabolomics data.
Converts files from Waters .raw format to mzData.
R functions for various plots.