{ "_id": "6a15482cacfb0bcc41d57fed", "Package": "mulea", "Type": "Package", "Title": "Enrichment Analysis Using Multiple Ontologies and False\nDiscovery Rate", "Version": "1.1.1", "Authors@R": "c(\nperson(\"Cezary\", \"Turek\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-1445-5378\")),\nperson(\"Marton\", \"Olbei\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4903-6237\")),\nperson(\"Tamas\", \"Stirling\", email = \"stirling.tamas@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8964-6443\")),\nperson(\"Gergely\", \"Fekete\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-9939-4860\")),\nperson(\"Ervin\", \"Tasnadi\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4713-5397\")),\nperson(\"Leila\", \"Gul\", role = \"aut\"),\nperson(\"Balazs\", \"Bohar\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3033-5448\")),\nperson(\"Balazs\", \"Papp\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3093-8852\")),\nperson(\"Wiktor\", \"Jurkowski\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-7820-1991\")),\nperson(\"Eszter\", \"Ari\", role = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-7774-1067\")))", "Description": "Background - Traditional gene set enrichment analyses are\ntypically limited to a few ontologies and do not account for\nthe interdependence of gene sets or terms, resulting in\novercorrected p-values. To address these challenges, we\nintroduce mulea, an R package offering comprehensive\noverrepresentation and functional enrichment analysis. Results\n- mulea employs a progressive empirical false discovery rate\n(eFDR) method, specifically designed for interconnected\nbiological data, to accurately identify significant terms\nwithin diverse ontologies. mulea expands beyond traditional\ntools by incorporating a wide range of ontologies, encompassing\nGene Ontology, pathways, regulatory elements, genomic\nlocations, and protein domains. This flexibility enables\nresearchers to tailor enrichment analysis to their specific\nquestions, such as identifying enriched transcriptional\nregulators in gene expression data or overrepresented protein\ndomains in protein sets. To facilitate seamless analysis, mulea\nprovides gene sets (in standardised GMT format) for 27 model\norganisms, covering 22 ontology types from 16 databases and\nvarious identifiers resulting in almost 900 files.\nAdditionally, the muleaData ExperimentData Bioconductor package\nsimplifies access to these pre-defined ontologies. Finally,\nmulea's architecture allows for easy integration of\nuser-defined ontologies, or GMT files from external sources\n(e.g., MSigDB or Enrichr), expanding its applicability across\ndiverse research areas. Conclusions - mulea is distributed as a\nCRAN R package. It offers researchers a powerful and flexible\ntoolkit for functional enrichment analysis, addressing\nlimitations of traditional tools with its progressive eFDR and\nby supporting a variety of ontologies. Overall, mulea fosters\nthe exploration of diverse biological questions across various\nmodel organisms.", "biocViews": "Annotation, DifferentialExpression, GeneExpression,\nGeneSetEnrichment, GO, GraphAndNetwork, MultipleComparison,\nPathways, Reactome, Software, Transcription, Visualization", "License": "GPL-2", "VignetteBuilder": "knitr", "URL": "https://github.com/ELTEbioinformatics/mulea", "BugReports": "https://github.com/ELTEbioinformatics/mulea/issues", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://eltebioinformatics.r-universe.dev", "Date/Publication": "2026-01-26 11:29:53 UTC", "RemoteUrl": "https://github.com/eltebioinformatics/mulea", "RemoteRef": "HEAD", "RemoteSha": "e23181f37e54a51e57e746b372d6a187be0e79e7", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-26 06:56:09 UTC", "User": "root" }, "Author": "Cezary Turek [aut] (ORCID: ),\nMarton Olbei [aut] (ORCID: ),\nTamas Stirling [aut, cre] (ORCID:\n),\nGergely Fekete [aut] (ORCID: ),\nErvin Tasnadi [aut] (ORCID: ),\nLeila Gul [aut],\nBalazs Bohar [aut] (ORCID: ),\nBalazs Papp [aut] (ORCID: ),\nWiktor Jurkowski [aut] (ORCID: ),\nEszter Ari [aut, cph] (ORCID: )", "Maintainer": "Tamas Stirling ", "MD5sum": "581c0844fbd437953bcfaa247b5d620a", "_user": "eltebioinformatics", "_type": "src", "_file": "mulea_1.1.1.tar.gz", "_fileid": "f862d5afeb055ac9ad225c0b84f1a300a2a8d76adb6b7a594fe626570cbabaf3", "_filesize": 1478730, "_sha256": "f862d5afeb055ac9ad225c0b84f1a300a2a8d76adb6b7a594fe626570cbabaf3", "_created": "2026-05-26T06:56:09.000Z", "_published": "2026-05-26T07:13:48.224Z", "_distro": "noble", "_jobs": [ { "job": 77822903355, "time": 277, "config": "linux-devel-arm64", "r": 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"author": " Cezary Turek, Márton Ölbei, Tamás Stirling (stirling.tamas@gmail.com), Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski & Eszter Ari ", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Usage", "Importing the Ontology", "Alternative 1: Importing the Ontology from a GMT File", "A) mulea GMT File", "B) Enrichr GMT File", "C) MsigDB GMT File", "Alternative 2: Importing the Ontology with the muleaData Package", "Filtering the Ontology", "Saving the Ontology as a GMT file", "Converting a List to an Ontology Object", "The Differential Expression Dataset to Analyse", "The Unordered Set-Based Overrepresentation Analysis (ORA)", "Reading the Target and the Background Sets from Text Files", "Performing the OverRepresentation Analysis", "Examining the ORA Result", "Visualising the ORA Result", "Comparing the significant results when applying the eFDR to the Benjamini-Hochberg and the Bonferroni corrections", "Gene Set Enrichment Analysis (GSEA)", "Reading the Tab Delimited File Containing the Ordered Set", "Performing the Gene Set Enrichment Analysis", "Examining the GSEA Results", "Visualising the GSEA Results", "Formatting the Results of a Differential Expression Analysis", "Understanding the Differential Expression Results Table", "Data Preparation:", "Preparing Input Data for the ORA", "Target Set", "Background Set", "Preparing Input Data for the GSEA", "Session Info", "How to Cite the mulea Package?", "References" ], "created": "2024-02-02 14:31:02", "modified": "2024-11-12 10:45:05", "commits": 20 } ], "_score": 6.666517980554881, "_indexed": true, "_nocasepkg": "mulea", "_universes": [ "eltebioinformatics", "stitam" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-05-26T06:59:23.000Z", "distro": "noble", "arch": "aarch64", "commit": "e23181f37e54a51e57e746b372d6a187be0e79e7", "fileid": "f100d349238c6e8ed895d55a0251c2c420d6f274ed61a8324e92368abfec385c", 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