Package: goatea 2.0.0

Maurits Unkel

goatea: Interactive Exploration of GSEA by the GOAT Method

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>.

Authors:Maurits Unkel [aut, cre, fnd, cph]

goatea_2.0.0.tar.gz
goatea_2.0.0.zip(r-4.7)goatea_2.0.0.zip(r-4.6)goatea_2.0.0.zip(r-4.5)
goatea_2.0.0.tgz(r-4.6-any)goatea_2.0.0.tgz(r-4.5-any)
goatea_2.0.0.tar.gz(r-4.7-any)goatea_2.0.0.tar.gz(r-4.6-any)
goatea_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
goatea/json (API)
NEWS

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

Bug tracker:https://github.com/mauritsunkel/goatea/issues

Pkgdown/docs site:https://mauritsunkel.github.io

Datasets:

On BioConductor:goatea-2.1.0(bioc 3.24)goatea-2.0.0(bioc 3.23)

genesetenrichmentnetworkenrichmentvisualizationshinyappsguitranscriptomicsgeneticsfunctionalgenomicsdifferentialexpressionnetwork

5.34 score 2 stars 3 scripts 56 downloads 25 exports 188 dependencies

Last updated from:8b7ad774dd (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE338
linux-devel-x86_64NOTE473
source / vignettesOK483
linux-release-x86_64NOTE438
macos-release-arm64NOTE383
macos-oldrel-arm64NOTE323
windows-develNOTE693
windows-releaseNOTE695
windows-oldrelNOTE641
wasm-releaseOK303

Exports:%>%calculate_geneSetRatiocolorifyfile_extensionfilter_enrichmentget_base_folderget_ppigraphget_string_ppiget_terms_by_keywordsget_visNetworkhexcolor2rgbaplot_ComplexHeatmapplot_EnhancedVolcanoplot_gene_effectsize_ComplexHeatmapplot_genelists_overlap_upsetjsplot_splitdotplot_termtreeprocess_string_inputread_validate_genelistrun_genelists_overlaprun_geneset_enrichmentscale_values_betweenset_significant_N_geneswrap_hovertipwrap_loader

Dependencies:aisdkAnnotationDbiapeaplotarrowaskpassassertthatbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcallrcellrangercirclizecliclisymbolsclueclusterclusterProfilercodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIdigestdoParallelDOSEdplyrDTEnhancedVolcanoenrichitenrichplotevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforeachfsgdtoolsgenericsGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggtangleggtreeGlobalOptionsglueGO.dbgoatGOSemSimgraphlayoutsgridBasegridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphInteractiveComplexHeatmapIRangesisobanditeratorsjquerylibjsonlitekableExtraKEGGRESTknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmatrixStatsmemoisemimeMonoPolynlmeopensslopenxlsxorg.Ce.eg.dborg.Dm.eg.dborg.Dr.eg.dborg.Hs.eg.dborg.Mm.eg.dborg.Mmu.eg.dborg.Pt.eg.dborg.Rn.eg.dbotelpatchworkpheatmappillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrquadprogqvalueR6rappdirsRColorBrewerRcppRcppArmadilloreadxlrematchreshape2rjsonrlangrmarkdownRSQLiterstudioapiS4VectorsS7sassscalesscatterpieSeqinfoshapeshinyshinydashboardshinyjquishinyjssourcetoolsstringistringrsvglitesyssystemfontstextshapingtibbletidydrtidygraphtidyrtidyselecttidytreetinytextreeiotreemaptweenrupsetjsutf8vctrsviridisviridisLitevisNetworkwithrwritexlxfunxml2xtableXVectoryamlyulab.utilszip

goatea GUI vignette

Maurits Unkel

Rendered fromgoatea_GUI.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2026-03-09

goatea vignette

Maurits Unkel

Rendered fromgoatea.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2025-04-24

Readme and manuals

Help Manual

Help pageTopics
Calculate geneSetRatio per gene per enrichment contrastcalculate_geneSetRatio
Create and/or modify color/gradient palettescolorify
Colorify colorRamp between colors mapping to breakpoint valuescolorify_map
Display R grDevices palettesdisplay_palettes
Example Colameo MS dataexample_Colameo_MS
Example Colameo RNA dataexample_Colameo_RNA
An example enrichmentexample_enrichment
An example genelistexample_genelist
An example genes overviewexample_genes_overview
Example genesetsexample_genesets
An example ppi dataexample_ppi_data
Get file extensionfile_extension
Filter enrichmentfilter_enrichment
Set base folderget_base_folder
Get PPI igraphget_ppigraph
Get STRING database Protein-Protein Interactionsget_string_ppi
Get term names by searching with (partial) keywordsget_terms_by_keywords
Get visNetwork graphget_visNetwork
Server for goatea packagegoatea_server
UI for GOATEA packagegoatea_ui
Hex code colors to rgba formathexcolor2rgba
Palette original name mappingpalette_name_mapping
Plot ComplexHeatmapplot_ComplexHeatmap
Plot EnhancedVolcanoplot_EnhancedVolcano
Plot gene2effectsize ComplexHeatmapplot_gene_effectsize_ComplexHeatmap
Visualize genelists gene overlap in an interactive UpSet plotplot_genelists_overlap_upsetjs
Plot splitdot plotplot_splitdot
Plot semantic similarity termtreeplot_termtree
Process Shiny area input stringprocess_string_input
Read and validate a table with genes (that should be tested in overrepresentation-analysis) for compatibility with this R package#'read_validate_genelist
Rename the gene overviewrename_gene_overview
Create gene overview through overlapping genelists information by overlapping significant genesrun_genelists_overlap
Perform geneset enrichment testing using any supported methodrun_geneset_enrichment
Scale values between given min/maxscale_values_between
Set significant and number of genesset_significant_N_genes
Wrap Shiny UI element with a hoverable tooltip contained in html div tagswrap_hovertip
Wrap Shiny UI element with a loading spinner contained in html div tagswrap_loader