mulea: Enrichment Analysis using Multiple Ontologies and FDR Correction

Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce 'mulea', an R package offering comprehensive overrepresentation and functional enrichment analysis. 'mulea' employs an innovative empirical false discovery rate (eFDR) correction method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. Beyond conventional tools, 'mulea' incorporates a wide range of ontologies encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility empowers 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 standardized GMT format) for 27 model organisms, covering 16 databases and various identifiers. Additionally, the 'muleaData' ExperimentData Bioconductor package simplifies access to these 879 pre-defined ontologies. Furthermore, 'mulea”s architecture allows for easy integration of user-defined ontologies, expanding its applicability across diverse research areas.

Version: 1.0.1
Depends: R (≥ 4.0.0)
Imports: data.table (≥ 1.13.0), dplyr, fgsea (≥ 1.0.2), ggplot2, ggraph (≥ 2.0.3), magrittr (≥ 2.0.3), methods, parallel (≥ 4.0.2), plyr (≥ 1.8.4), Rcpp, readr, rlang, scales, stats, stringi, tibble, tidygraph, tidyverse
LinkingTo: Rcpp
Suggests: devtools, knitr, rmarkdown, testthat (≥ 3.1.4)
Published: 2024-06-19
DOI: 10.32614/CRAN.package.mulea
Author: Cezary Turek ORCID iD [aut], Marton Olbei ORCID iD [aut], Tamas Stirling ORCID iD [aut, cre], Gergely Fekete ORCID iD [aut], Ervin Tasnadi ORCID iD [aut], Leila Gul [aut], Balazs Bohar ORCID iD [aut], Balazs Papp ORCID iD [aut], Wiktor Jurkowski ORCID iD [aut], Eszter Ari ORCID iD [aut, cph]
Maintainer: Tamas Stirling <stirling.tamas at gmail.com>
BugReports: https://github.com/ELTEbioinformatics/mulea/issues
License: GPL-2
URL: https://github.com/ELTEbioinformatics/mulea
NeedsCompilation: yes
Citation: mulea citation info
Materials: NEWS
CRAN checks: mulea results

Documentation:

Reference manual: mulea.pdf
Vignettes: mulea

Downloads:

Package source: mulea_1.0.1.tar.gz
Windows binaries: r-devel: mulea_1.0.0.zip, r-release: mulea_1.0.1.zip, r-oldrel: mulea_1.0.1.zip
macOS binaries: r-release (arm64): mulea_1.0.1.tgz, r-oldrel (arm64): mulea_1.0.1.tgz, r-release (x86_64): mulea_1.0.1.tgz, r-oldrel (x86_64): mulea_1.0.1.tgz
Old sources: mulea archive

Linking:

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