  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.
