goatea
This is the development version of goatea; for the stable release version, see goatea.
Interactive Exploration of GSEA by the GOAT Method
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 2.1.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | goatea_2.1.0.tar.gz |
| Windows Binary (x86_64) | goatea_2.1.0.zip |
| macOS Binary (big-sur-x86_64) | goatea_2.1.0.tgz |
| macOS Binary (sonoma-arm64) | goatea_2.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/goatea |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/goatea |
| Bioc Package Browser | https://code.bioconductor.org/browse/goatea/ |
| Package Short Url | https://bioconductor.org/packages/goatea/ |
| Package Downloads Report | Download Stats |