Package: mulea
Type: Package
Title: Enrichment Analysis using Multiple Ontologies and FDR Correction
Version: 1.0.1
Date: 2024-06-18
Authors@R: c(
    person("Cezary", "Turek", role =  "aut",
        comment = c(ORCID = "0000-0002-1445-5378")),
    person("Marton", "Olbei", role = "aut",
        comment = c(ORCID = "0000-0002-4903-6237")),
    person("Tamas", "Stirling", email = "stirling.tamas@gmail.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-8964-6443")),
    person("Gergely", "Fekete", role = "aut",
        comment = c(ORCID = "0000-0001-9939-4860")),
    person("Ervin", "Tasnadi", role = "aut",
        comment = c(ORCID = "0000-0002-4713-5397")),
    person("Leila", "Gul", role = "aut"),
    person("Balazs", "Bohar", role = "aut",
        comment = c(ORCID = "0000-0002-3033-5448")),
    person("Balazs", "Papp", role = "aut",
        comment = c(ORCID = "0000-0003-3093-8852")),
    person("Wiktor", "Jurkowski", role = "aut",
        comment = c(ORCID = "0000-0002-7820-1991")),
    person("Eszter", "Ari", role = c("aut", "cph"),
        comment = c(ORCID = "0000-0001-7774-1067")))
Description: 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.
biocViews: Annotation, DifferentialExpression, GeneExpression,
        GeneSetEnrichment, GO, GraphAndNetwork, MultipleComparison,
        Pathways, Reactome, Software, Transcription, Visualization
License: GPL-2
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
Suggests: devtools, knitr, rmarkdown, testthat (>= 3.1.4)
LinkingTo: Rcpp
VignetteBuilder: knitr
URL: https://github.com/ELTEbioinformatics/mulea
BugReports: https://github.com/ELTEbioinformatics/mulea/issues
RoxygenNote: 7.3.1
Config/testthat/edition: 3
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-06-18 12:36:13 UTC; tamas
Author: Cezary Turek [aut] (<https://orcid.org/0000-0002-1445-5378>),
  Marton Olbei [aut] (<https://orcid.org/0000-0002-4903-6237>),
  Tamas Stirling [aut, cre] (<https://orcid.org/0000-0002-8964-6443>),
  Gergely Fekete [aut] (<https://orcid.org/0000-0001-9939-4860>),
  Ervin Tasnadi [aut] (<https://orcid.org/0000-0002-4713-5397>),
  Leila Gul [aut],
  Balazs Bohar [aut] (<https://orcid.org/0000-0002-3033-5448>),
  Balazs Papp [aut] (<https://orcid.org/0000-0003-3093-8852>),
  Wiktor Jurkowski [aut] (<https://orcid.org/0000-0002-7820-1991>),
  Eszter Ari [aut, cph] (<https://orcid.org/0000-0001-7774-1067>)
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Repository: CRAN
Date/Publication: 2024-06-19 08:40:11 UTC
Built: R 4.3.3; aarch64-apple-darwin20; 2024-06-19 11:59:08 UTC; unix
Archs: mulea.so.dSYM
