maplet: An extensible R toolbox for modular and reproducible omics pipelines.

This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. 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 individual maintenance of 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.