goatea
This is the released version of goatea; for the devel version, see goatea.
Interactive Exploration of GSEA by the GOAT Method
Bioconductor version: Release (3.23)
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>.
Author: Maurits Unkel [aut, cre, fnd, cph] 
Maintainer: Maurits Unkel <mauritsunkel at gmail.com>
citation("goatea")):Maurits Unkel. goatea: Interactive Exploration of GSEA by the GOAT Method. doi:10.18129/B9.bioc.goatea, R package version 2.0.0, https://bioconductor.org/packages/goatea.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("goatea")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("goatea")| 1. GOATEA GUI & installation | HTML | R Script |
| 2. GOATEA R package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, FunctionalGenomics, GUI, GeneSetEnrichment, Genetics, Network, NetworkEnrichment, ShinyApps, Software, Transcriptomics, Visualization |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Apache License (>= 2) |
| 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) |
| System Requirements | |
| URL | https://github.com/mauritsunkel/goatea https://mauritsunkel.github.io/goatea/ |
| Bug Reports | https://github.com/mauritsunkel/goatea/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | goatea_2.0.0.tar.gz |
| Windows Binary (x86_64) | goatea_2.0.0.zip |
| macOS Binary (big-sur-x86_64) | goatea_2.0.0.tgz |
| macOS Binary (sonoma-arm64) | goatea_2.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/goatea |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/goatea |
| Package Short Url | https://bioconductor.org/packages/goatea/ |
| Package Downloads Report | Download Stats |