Package: MetaboDynamics 0.99.20

Katja Danielzik

MetaboDynamics: Bayesian analysis of longitudinal metabolomics data

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.

Authors:Katja Danielzik [aut, cre], Simo Kitanovski [ctb], Johann Matschke [ctb], Daniel Hoffmann [ctb]

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MetaboDynamics.pdf |MetaboDynamics.html✨
MetaboDynamics/json (API)
NEWS

# Install 'MetaboDynamics' in R:
install.packages('MetaboDynamics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/katjadanielzik/metabodynamics/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:MetaboDynamics-0.99.18(bioc 3.21)

softwaremetabolomicsbayesianfunctionalpredictionmultiplecomparisonkeggdynamicsfunctional-analysislongitudinal-analysismetabolomics-datametabolomics-pipelinecpp

4.90 score 4 stars 3 scripts 67 downloads 13 exports 85 dependencies

Last updated 6 days agofrom:cddeae644e. Checks:1 OK, 5 NOTE, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-win-x86_64NOTEFeb 15 2025
R-4.5-mac-x86_64WARNINGFeb 15 2025
R-4.5-mac-aarch64WARNINGFeb 15 2025
R-4.5-linux-x86_64NOTEFeb 15 2025
R-4.4-win-x86_64NOTEFeb 15 2025
R-4.4-mac-x86_64NOTEFeb 15 2025
R-4.4-mac-aarch64NOTEFeb 15 2025

Exports:compare_dynamicscompare_metabolitesdiagnostics_dynamicsestimates_dynamicsfit_dynamics_modelget_ORA_annotationsheatmap_dynamicsheatmap_metabolitesORA_hypergeometricplot_diagnosticsplot_estimatesplot_ORAplot_PPC

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiostringscallrcheckmateclicolorspacecpp11crayoncurlDelayedArraydescdistributionaldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehttrinlineIRangesisobandjsonliteKEGGRESTlabelinglatticelifecycleloomagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmenumDerivopensslpillarpkgbuildpkgconfigpngposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS4ArraysS4VectorsscalesSparseArrayStanHeadersstringistringrSummarizedExperimentsystensorAtibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector

MetaboDynamics: analyzing longitudinal metabolomics data with probabilistic models

Katja Danielzik ([email protected])

Rendered fromMetaboDynamics.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2024-12-20
Started: 2024-12-20