maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines

Area of Science:

• Bioinformatics
• Computational Biology
• Data Science

Background:

• Metabolomics data analysis requires robust and reproducible statistical pipelines.
• Existing tools may lack modularity or comprehensive functionality for complex workflows.
• Centralized frameworks are needed for managing data, analysis steps, and results.

Purpose of the Study:

• To present maplet, an open-source R package designed for creating customizable and fully reproducible statistical pipelines in metabolomics.
• To provide a centralized framework for managing metabolomics data, analysis steps, results, and visualizations.

Main Methods:

• The maplet package is implemented in R, utilizing the SummarizedExperiment data structure.
• It features a modular design with over 90 individual functions.
• The package supports collaborative development by lowering contribution barriers.

Main Results:

• maplet enables the creation of highly customizable and reproducible metabolomics analysis pipelines.
• Its modularity enhances code quality and facilitates collaborative development.
• The package integrates a wide range of statistical approaches and data visualization techniques.

Conclusions:

• maplet offers a comprehensive and flexible solution for metabolomics data analysis.
• The package promotes reproducibility and collaboration in the field.
• Its extensive functionalities make it a valuable tool for researchers in metabolomics.