goatea
Interactive Exploration of GSEA by the GOAT Method
Bioconductor version: 3.23 · Package version: 2.0.0
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>.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("goatea")Details
| Maintainer | Maurits Unkel <mauritsunkel@gmail.com> |
| Author | Maurits Unkel [aut, cre, fnd, cph] (ORCID: <https://orcid.org/0000-0003-1920-6001>) |
| License | Apache License (>= 2) |
| URL | https://github.com/mauritsunkel/goatea, https://mauritsunkel.github.io/goatea/ |
| Bug Reports | https://github.com/mauritsunkel/goatea/issues |
| Downloads rank | 97 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, FunctionalGenomics, GUI, GeneSetEnrichment, Genetics, Network, NetworkEnrichment, ShinyApps, Software, Transcriptomics, Visualization |
Documentation
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Dependencies
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), data.table (>= 1.18.2.1), 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), plyr (>= 1.8.9), tibble (>= 3.2.1), rlang (>= 1.1.6), DOSE (>= 4.4.0), enrichplot (>= 1.30.4), clusterProfiler (>= 4.18.4), EnhancedVolcano (>= 1.28.2), org.Hs.eg.db (>= 3.22.0), org.Mm.eg.db (>= 3.22.0), org.Dm.eg.db (>= 3.22.0), org.Mmu.eg.db (>= 3.22.0), org.Rn.eg.db (>= 3.22.0), org.Ce.eg.db (>= 3.22.0), org.Pt.eg.db (>= 3.22.0), org.Dr.eg.db (>= 3.22.0)