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To address these challenges, we introduce mulea, an R package offering     comprehensive overrepresentation and functional enrichment analysis.     Results - mulea employs a progressive empirical false discovery rate     (eFDR) method, specifically designed for interconnected biological data,     to accurately identify significant terms within diverse ontologies. mulea     expands beyond traditional tools by incorporating a wide range of     ontologies, encompassing Gene Ontology, pathways, regulatory elements,     genomic locations, and protein domains. This flexibility enables     researchers to tailor enrichment analysis to their specific questions,     such as identifying enriched transcriptional regulators in gene expression     data or overrepresented protein domains in protein sets. To facilitate     seamless analysis, mulea provides gene sets (in standardised GMT format)     for 27 model organisms, covering 22 ontology types from 16 databases and     various identifiers resulting in almost 900 files. Additionally, the     muleaData ExperimentData Bioconductor package simplifies access to these     pre-defined ontologies. Finally, mulea's architecture allows for easy     integration of user-defined ontologies, or GMT files from external     sources (e.g., MSigDB or Enrichr), expanding its applicability across     diverse research areas. Conclusions - mulea is distributed as a CRAN R     package. It offers researchers a powerful and flexible toolkit for     functional enrichment analysis, addressing limitations of traditional     tools with its progressive eFDR and by supporting a variety of ontologies.     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