EnrichMET: R Package for Integrated Pathway and Network Analysis for Metabolomics

Advances in metabolomics have significantly improved our understanding of cellular processes by enabling the identification of hundreds of metabolites in a single experiment. These developments provide valuable insights into complex metabolic networks. Pathway Enrichment Analysis (PEA) is essential for connecting identified metabolites with biological pathways, uncovering meaningful relationships, and revealing underlying metabolic mechanisms. However, existing tools, often require multiple steps, rely on web-based interfaces, and require R packages that can be challenging to install due to outdated or missing dependencies. This hampers both reproducibility and efficiency. To overcome these limitations, we introduce EnrichMet, an R package designed for efficient and reproducible pathway, metabolite set enrichment analysis (MetSEA). The package integrates fgsea for rapid MetSEA and igraph for topology-based metrics, enabling comprehensive integration of metabolomics data. EnrichMet utilizes curated pathway data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and employs Fisher’s Exact Test to identify significantly enriched pathways. Through a case study on experimental metabolomics datasets, we demonstrate the robustness and efficiency of EnrichMet, benchmarking it against existing tools. The results show that EnrichMet provides accurate and comprehensive pathway enrichment outcomes while reducing computational time and user effort. Moreover, its flexible framework allows EnrichMet to be adaptable to a broad range of data types and applications beyond KEGG. By streamlining the pathway analysis process, EnrichMet enables researchers to derive deeper insights from metabolomics data, promoting reproducible and efficient research practices.