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
QC systems for metabolomics studies.
Retention time prediction system for chromatography.
Shiny app to decompose a mass to possible molecular formulas.
Mass spectrometry data curation tools.
Peaklist Annotator and Browser.
Waters Logbook. Automatic logbook for Waters RAW files.
R Packages
Metabolomics Data Pre-Processing
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.
Data Analysis & Visualization
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.
Online book reviewing R and Bioconductor packages for metabolomics data analysis.
Data massaging utilities for metabolomics: batch correction, NA imputation, normalization, fold change calculation, and dendrogram preparation for heatmaps.
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.