MetaboDynamics
This is the development version of MetaboDynamics; for the stable release version, see MetaboDynamics.
Bayesian analysis of longitudinal metabolomics data
Bioconductor version: Development (3.24)
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("MetaboDynamics")):Katja Danielzik. MetaboDynamics: Bayesian analysis of longitudinal metabolomics data. doi:10.18129/B9.bioc.MetaboDynamics, R package version 2.3.13, 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")
## The following initializes the development version of Bioconductor
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")| 2. MetaboDynamics_dataframes | HTML | R Script |
| 3. MetaboDynamics_Guide_to_prior_setting | HTML | R Script |
| 1. MetaboDynamics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Clustering, FunctionalPrediction, KEGG, Metabolomics, MultipleComparison, Pathways, Software, TimeCourse |
| Version | 2.3.13 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| 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, rlang, ape, ggtree, patchwork |
| System Requirements | GNU make |
| URL | https://github.com/KatjaDanielzik/MetaboDynamics |
| Bug Reports | https://github.com/KatjaDanielzik/MetaboDynamics/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| Linking To | 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) |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MetaboDynamics_2.3.13.tar.gz |
| Windows Binary (x86_64) | MetaboDynamics_2.3.13.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MetaboDynamics_2.3.13.tgz |
| macOS Binary (sonoma-arm64) | MetaboDynamics_2.3.13.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaboDynamics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaboDynamics |
| Package Short Url | https://bioconductor.org/packages/MetaboDynamics/ |
| Package Downloads Report | Download Stats |