MetaboDynamics
This is the released version of MetaboDynamics; for the devel version, see MetaboDynamics.
All Bioconductor versions of MetaboDynamics
3.24 (devel), 3.23 (release), 3.22, 3.21
Bayesian analysis of longitudinal metabolomics data
Bioconductor version: 3.23 · Package version: 2.2.1
MetaboDynamics is an R-package that provides a framework of probabilistic models to analyze longitudinal metabolomics data. It enables robust estimation of mean concentrations despite varying spread between timepoints and reports differences between timepoints as well as metabolite specific dynamics profiles that can be used for identifying "dynamics clusters" of metabolites of similar dynamics. Provides probabilistic over-representation analysis of KEGG functional modules and pathways as well as comparison between clusters of different experimental conditions.
Author: Katja Danielzik [aut, cre] 
, Simo Kitanovski [ctb] , Johann Matschke [ctb] , Daniel Hoffmann [ctb]
Maintainer: Katja Danielzik <katja.danielzik at uni-due.de>
Citation
From within R, enter citation("MetaboDynamics"):
Katja Danielzik. MetaboDynamics: Bayesian analysis of longitudinal metabolomics data. doi:10.18129/B9.bioc.MetaboDynamics, R package version 2.2.1, https://bioconductor.org/packages/MetaboDynamics.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MetaboDynamics")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.2.1 |
| License | GPL (>= 3) |
| URL | https://github.com/KatjaDanielzik/MetaboDynamics |
| Bug Reports | https://github.com/KatjaDanielzik/MetaboDynamics/issues |
| System Requirements | GNU make |
| Last updated | 2026-09-07 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2076 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, Clustering, FunctionalPrediction, KEGG, Metabolomics, MultipleComparison, Pathways, Software, TimeCourse |
| Package Short Url | https://bioconductor.org/packages/MetaboDynamics/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MetaboDynamics")| MetaboDynamics: analyzing longitudinal metabolomics data with probabilistic models | HTML | R Script |
| Using MetaboDynamics with data frames | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | MetaboDynamics_2.2.1.tar.gz |
| Windows binary (x86_64) | MetaboDynamics_2.2.1.zip |
| macOS binary (arm64) | MetaboDynamics_2.2.1.tgz |
| macOS binary (x86_64) | MetaboDynamics_2.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaboDynamics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaboDynamics |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |
Dependencies
Depends: R (>= 4.4.0)
Imports: dplyr, ggplot2, KEGGREST, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.4.0), S4Vectors, stringr, SummarizedExperiment, tidyr, dynamicTreeCut, rlang, ape, ggtree, patchwork
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)