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 (3.22)
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)
Author: Maurits Unkel [aut, cre, fnd, cph]
Maintainer: Maurits Unkel <mauritsunkel at gmail.com>
citation("goatea")):
Installation
To install this package, start R (version "4.5") 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
| Reference Manual |
Details
| biocViews | DifferentialExpression, FunctionalGenomics, GUI, GeneSetEnrichment, Genetics, Network, NetworkEnrichment, ShinyApps, Software, Transcriptomics, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| 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), ComplexHeatmap(>= 2.24.0), InteractiveComplexHeatmap(>= 1.12.0), EnhancedVolcano(>= 1.22.0), 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) |
| System Requirements | |
| URL | https://github.com/mauritsunkel/goatea |
| Bug Reports | https://github.com/mauritsunkel/goatea/issues |
See More
| Suggests | 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |