Package: goatea
Type: Package
Title: Interactive Exploration of GSEA by the GOAT Method
Version: 1.1.3
Authors@R: 
    person("Maurits", "Unkel",
		   role = c("aut", "cre", "fnd", "cph"),
		   email = "mauritsunkel@gmail.com",
		   comment = c(ORCID = "0000-0003-1920-6001"))
Description: Geneset Ordinal Association Test Enrichment Analysis (GOATEA) provides a 'Shiny' interface with interactive visualizations and utility functions for performing and exploring automated gene set enrichment analysis using the 'GOAT' package. 
    'GOATEA' is designed to support large-scale and user-friendly enrichment workflows across multiple gene lists and comparisons, with flexible plotting and output options.
    Visualizations pre-enrichment include interactive 'Volcano' and 'UpSet' (overlap) plots. Visualizations post-enrichment include interactive geneset dotplot, geneset treeplot, gene-effectsize heatmap, gene-geneset heatmap and 'STRING' database of protein-protein-interactions network graph. 
	'GOAT' reference: Frank Koopmans (2024) <doi:10.1038/s42003-024-06454-5>.
URL: https://github.com/mauritsunkel/goatea
BugReports: https://github.com/mauritsunkel/goatea/issues
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
biocViews: GeneSetEnrichment, NetworkEnrichment, Visualization, ShinyApps, GUI, Transcriptomics, Genetics, FunctionalGenomics, DifferentialExpression, Network
Depends: 
    R (>= 4.5.0),
	dplyr (>= 1.1.4)
Imports:
    goat (>= 1.0),
    shiny (>= 1.10.0),
    shinyjs (>= 2.1.0),
    shinyjqui (>= 0.4.1),
    shinydashboard (>= 0.7.2),
    openxlsx (>= 4.2.7.1),
    upsetjs (>= 1.11.1),
    ComplexHeatmap (>= 2.24.0),
    InteractiveComplexHeatmap (>= 1.12.0),
    tidyr (>= 1.3.1),
    purrr (>= 1.0.2),
    ggplot2 (>= 3.5.1),
    plotly (>= 4.10.4),
    igraph (>= 2.1.4),
    visNetwork (>= 2.1.2),
    arrow (>= 18.1.0.1),
    htmltools (>= 0.5.8.1),
    methods (>= 4.5.0),
    AnnotationDbi (>= 1.69.1),
    DT (>= 0.33),
    enrichplot (>= 1.27.4),
    plyr (>= 1.8.9),
    tibble (>= 3.2.1),
	rlang (>= 1.1.6)
Suggests:
	EnhancedVolcano,
    org.Hs.eg.db,
    org.Mm.eg.db,
	org.Dm.eg.db,
	org.Mmu.eg.db,
	org.Rn.eg.db,
	org.Ce.eg.db,
	org.Pt.eg.db,
	org.Dr.eg.db,
	knitr,
	rmarkdown,
	BiocStyle
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/goatea
git_branch: devel
git_last_commit: fb910ce
git_last_commit_date: 2025-11-12
Repository: Bioconductor 3.23
