<tt>maplet</tt>: an extensible R toolbox for modular and reproducible metabolomics pipelines
Kelsey Chetnik, Elisa Benedetti, Daniel P. Gomari, Annalise Schweickart, Richa Batra, Mustafa Büyüközkan, Zeyu Wang, Matthias Arnold, Jonas Zierer, Karsten Suhre, Jan Krumsiek
Abstract
This article presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for metabolomics data analysis. It builds on the SummarizedExperiment data structure to create a centralized pipeline framework for storing data, analysis steps, results and visualizations. maplet's key design feature is its modularity, which offers several advantages, such as ensuring code quality through the maintenance of individual functions and promoting collaborative development by removing technical barriers to code contribution. With over 90 functions, the package includes a wide range of functionalities, covering many widely used statistical approaches and data visualization techniques. AVAILABILITY AND IMPLEMENTATION: The maplet package is implemented in R and freely available at https://github.com/krumsieklab/maplet.