Package: mulea 1.1.0

Tamas Stirling

mulea: Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Background - 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. 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. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

Authors:Cezary Turek [aut], Marton Olbei [aut], Tamas Stirling [aut, cre], Gergely Fekete [aut], Ervin Tasnadi [aut], Leila Gul [aut], Balazs Bohar [aut], Balazs Papp [aut], Wiktor Jurkowski [aut], Eszter Ari [aut, cph]

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mulea.pdf |mulea.html
mulea/json (API)
NEWS

# Install 'mulea' in R:
install.packages('mulea', repos = c('https://eltebioinformatics.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/eltebioinformatics/mulea/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationbioconductor-packageenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomics

7.32 score 21 stars 33 scripts 340 downloads 12 exports 131 dependencies

Last updated 1 months agofrom:47dcc2878a. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-win-x86_64OKOct 24 2024
R-4.5-linux-x86_64OKOct 24 2024
R-4.4-win-x86_64OKOct 24 2024
R-4.4-mac-x86_64OKOct 24 2024
R-4.4-mac-aarch64OKOct 24 2024
R-4.3-win-x86_64OKOct 24 2024
R-4.3-mac-x86_64OKOct 24 2024
R-4.3-mac-aarch64OKOct 24 2024

Exports:filter_ontologygsealist_to_gmtoraplot_barplotplot_graphplot_heatmapplot_lollipopread_gmtreshape_resultsrun_testwrite_gmt

Dependencies:askpassbackportsbase64encBHBiocParallelbitbit64blobbroombslibcachemcallrcellrangerclicliprcodetoolscolorspaceconflictedcowplotcpp11crayoncurldata.tableDBIdbplyrdigestdplyrdtplyrevaluatefansifarverfastmapfastmatchfgseafontawesomeforcatsformatRfsfutile.loggerfutile.optionsgarglegenericsggforceggplot2ggraphggrepelgluegoogledrivegooglesheets4graphlayoutsgridExtragtablehavenhighrhmshtmltoolshttridsigraphisobandjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemodelrmunsellnlmeopensslpillarpkgconfigplyrpolyclipprettyunitsprocessxprogresspspurrrR6raggrappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrematchrematch2reprexrlangrmarkdownrstudioapirvestsassscalesselectrsnowstringistringrsyssystemfontstextshapingtibbletidygraphtidyrtidyselecttidyversetimechangetinytextweenrtzdbutf8uuidvctrsviridisviridisLitevroomwithrxfunxml2yaml

mulea

Rendered frommulea.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-09-24
Started: 2024-02-02

Readme and manuals

Help Manual

Help pageTopics
Filter Ontologyfilter_ontology
Gene Set Enrichment Analysis (GSEA)gsea gsea-class run_test,gsea-method
Convert a list to ontology (GMT) 'data.frame'.list_to_gmt
PRIVATE class : An S4 class to represent a Hypergeometric tests in mulea.MuleaHypergeometricTest MuleaHypergeometricTest-class run_test,MuleaHypergeometricTest-method
An S4 class to represent a set based tests in mulea.ora ora-class
Plot Barplotplot_barplot
Plot Graph (Network)plot_graph
Plot Heatmapplot_heatmap
Plot Lollipopplot_lollipop
Read GMT Fileread_gmt
Reshape Resultsreshape_results
Run enrichment analysis procedurerun_test run_test,ora-method
PRIVATE class : An S4 class to represent a Hypergeometric tests in mulea.run_test,SetBasedEnrichmentTest-method SetBasedEnrichmentTest SetBasedEnrichmentTest-class
PRIVATE class : An S4 class to represent a ranked based tests in mulea.run_test,SubramanianTest-method SubramanianTest SubramanianTest-class
Write GMT filewrite_gmt