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To address these challenges, we introduce\n                    <jats:italic>mulea<\/jats:italic>\n                    , an R package offering comprehensive overrepresentation and functional enrichment analysis.\n                    <jats:italic>mulea<\/jats:italic>\n                    employs a progressive\n                    <jats:italic>empirical false discovery rate (eFDR) method<\/jats:italic>\n                    , specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies.\n                    <jats:italic>mulea<\/jats:italic>\n                    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,\n                    <jats:italic>mulea<\/jats:italic>\n                    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\n                    <jats:italic>muleaData<\/jats:italic>\n                    ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally,\n                    <jats:italic>mulea<\/jats:italic>\n                    's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (\n                    <jats:italic>e.g.,<\/jats:italic>\n                    MSigDB or Enrichr), expanding its applicability across diverse research areas.\n                    <jats:italic>mulea<\/jats:italic>\n                    is distributed as a CRAN\n                    <jats:italic>R<\/jats:italic>\n                    package downloadable from\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cran.r-project.org\/web\/packages\/mulea\/\">https:\/\/cran.r-project.org\/web\/packages\/mulea\/<\/jats:ext-link>\n                    and\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ELTEbioinformatics\/mulea\">https:\/\/github.com\/ELTEbioinformatics\/mulea<\/jats:ext-link>\n                    . 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. Overall,\n                    <jats:italic>mulea<\/jats:italic>\n                    fosters the exploration of diverse biological questions across various model organisms.\n                  <\/jats:p>","DOI":"10.1186\/s12859-024-05948-7","type":"journal-article","created":{"date-parts":[[2024,10,18]],"date-time":"2024-10-18T13:02:27Z","timestamp":1729256547000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate"],"prefix":"10.1186","volume":"25","author":[{"given":"Cezary","family":"Turek","sequence":"first","affiliation":[]},{"given":"M\u00e1rton","family":"\u00d6lbei","sequence":"additional","affiliation":[]},{"given":"Tam\u00e1s","family":"Stirling","sequence":"additional","affiliation":[]},{"given":"Gergely","family":"Fekete","sequence":"additional","affiliation":[]},{"given":"Ervin","family":"Tasn\u00e1di","sequence":"additional","affiliation":[]},{"given":"Leila","family":"Gul","sequence":"additional","affiliation":[]},{"given":"Bal\u00e1zs","family":"Boh\u00e1r","sequence":"additional","affiliation":[]},{"given":"Bal\u00e1zs","family":"Papp","sequence":"additional","affiliation":[]},{"given":"Wiktor","family":"Jurkowski","sequence":"additional","affiliation":[]},{"given":"Eszter","family":"Ari","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,10,18]]},"reference":[{"key":"5948_CR1","doi-asserted-by":"publisher","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","volume":"4","author":"G Dennis","year":"2003","unstructured":"Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, et al. 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