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.
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softwaremetabolomicsbayesianfunctionalpredictionmultiplecomparisonkeggpathwaystimecourseclusteringdynamicsfunctional-analysislongitudinal-analysismetabolomics-datametabolomics-pipelineonetbbcpp
5.99 score 5 stars 5 scripts 318 downloads
BayesVolcano - Creating Volcano Plots from Bayesian Model Posteriors
Bayesian models are used to estimate effect sizes (e.g., gene expression changes, protein abundance differences, drug response effects) while accounting for uncertainty, small sample sizes, and complex experimental designs. However, Bayesian posteriors of models with many parameters are often difficult to interpret at a glance. One way to quickly identify important biological changes based on frequentist analysis are volcano plots (using fold-changes and p-values). Bayesian volcano plots bring together the explicit treatment of uncertainty in Bayesian models and the familiar visualization of volcano plots.
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bayesianposteriorvisualizationvolcano-plot
4.40 score 1 stars 280 downloads