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Bioconductor - MetaboDynamics (development version)

MetaboDynamics

This is the development version of MetaboDynamics; for the stable release version, see MetaboDynamics.

Bayesian analysis of longitudinal metabolomics data

Bioconductor version: Development (3.22)

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] ORCID: 0009-0007-5021-6212 , Simo Kitanovski [ctb] ORCID: 0000-0003-2909-5376 , Johann Matschke [ctb] ORCID: 0000-0003-4878-8741 , Daniel Hoffmann [ctb] ORCID: 0000-0003-2973-7869

Maintainer: Katja Danielzik <katja.danielzik at uni-due.de>

Citation (from within R, enter citation("MetaboDynamics")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MetaboDynamics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MetaboDynamics")
Details biocViews Bayesian, FunctionalPrediction, KEGG, Metabolomics, MultipleComparison, Pathways, Software, TimeCourse Version 1.1.1 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License GPL (>= 3) 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, dendextend, rlang System Requirements GNU make URL https://github.com/KatjaDanielzik/MetaboDynamics Bug Reports https://github.com/KatjaDanielzik/MetaboDynamics/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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