Package: mulea 1.1.1
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:
mulea_1.1.1.tar.gz
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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')) |
Bug tracker:https://github.com/eltebioinformatics/mulea/issues
annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationbioconductor-packageenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomics
Last updated 2 days agofrom:7ef142017b. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 19 2024 |
R-4.5-win-x86_64 | OK | Nov 19 2024 |
R-4.5-linux-x86_64 | OK | Nov 19 2024 |
R-4.4-win-x86_64 | OK | Nov 19 2024 |
R-4.4-mac-x86_64 | OK | Nov 19 2024 |
R-4.4-mac-aarch64 | OK | Nov 19 2024 |
R-4.3-win-x86_64 | OK | Nov 19 2024 |
R-4.3-mac-x86_64 | OK | Nov 19 2024 |
R-4.3-mac-aarch64 | OK | Nov 19 2024 |
Exports:filter_ontologygsealist_to_gmtoraplot_barplotplot_graphplot_heatmapplot_lollipopread_gmtreshape_resultsrun_testwrite_gmt
Dependencies:askpassbackportsbase64encBHBiocParallelbitbit64blobbroombslibcachemcallrcellrangerclicliprcodetoolscolorspaceconflictedcowplotcpp11crayoncurldata.tableDBIdbplyrdigestdplyrdtplyrevaluatefansifarverfastmapfastmatchfgseafontawesomeforcatsformatRfsfutile.loggerfutile.optionsgarglegenericsggforceggplot2ggraphggrepelgluegoogledrivegooglesheets4graphlayoutsgridExtragtablehavenhighrhmshtmltoolshttridsigraphisobandjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemodelrmunsellnlmeopensslpillarpkgconfigplyrpolyclipprettyunitsprocessxprogresspspurrrR6raggrappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrematchrematch2reprexrlangrmarkdownrstudioapirvestsassscalesselectrsnowstringistringrsyssystemfontstextshapingtibbletidygraphtidyrtidyselecttidyversetimechangetinytextweenrtzdbutf8uuidvctrsviridisviridisLitevroomwithrxfunxml2yaml
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Filter Ontology | filter_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 Barplot | plot_barplot |
Plot Graph (Network) | plot_graph |
Plot Heatmap | plot_heatmap |
Plot Lollipop | plot_lollipop |
Read GMT File | read_gmt |
Reshape Results | reshape_results |
Run enrichment analysis procedure | run_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 file | write_gmt |