MetaboDynamics
This is the development version of MetaboDynamics; to use it, please install the devel version of Bioconductor.
Bayesian analysis of longitudinal metabolomics data
Bioconductor version: Development (3.21)
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 and comparison betweeen clusters of different experimental conditions.
Author: Katja Danielzik [aut, cre] (ORCID:
Maintainer: Katja Danielzik <katja.danielzik at uni-due.de>
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")| 1. MetaboDynamics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, FunctionalPrediction, KEGG, Metabolomics, MultipleComparison, Software |
| Version | 0.99.18 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MetaboDynamics_0.99.18.tar.gz |
| Windows Binary (x86_64) | MetaboDynamics_0.99.18.zip |
| macOS Binary (x86_64) | MetaboDynamics_0.99.18.tgz |
| macOS Binary (arm64) | MetaboDynamics_0.99.18.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaboDynamics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaboDynamics |
| Bioc Package Browser | https://code.bioconductor.org/browse/MetaboDynamics/ |
| Package Short Url | https://bioconductor.org/packages/MetaboDynamics/ |
| Package Downloads Report | Download Stats |