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# goatea <img src="man/figures/logo.png" align="right" height="139" alt="" />
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 split term dotplot, geneset
hierarchical clustering treeplot, multi-genelist gene-effectsize
heatmap, enrichment overview gene-geneset heatmap and bottom-up
pathway-like STRING database of protein-protein-interactions network
graph.
# Installation
The development version of goatea is available through Github, goatea
will become available through Bioconductor.
``` r
## GOATEA installation requires the latest version of R and Rtools
## Rtools is needed for package compilation, to download and install visit:
# R: https://cran.r-project.org/mirrors.html
# Rtools: https://cran.r-project.org/bin/windows/Rtools/
## To install GOATEA from Bioconductor use:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("goatea")
# or via pak
pak::pkg_install('goatea', dependencies = TRUE, upgrade = TRUE)
## When GOATEA is on Bioconductor use:
# pak::pkg_install('goatea', dependencies = TRUE, upgrade = TRUE)
## goatea organism (taxid) genome wide annotation packages (org.Xx.eg.dg)
## goatea requires at least one of the following available organism packages:
# Human (9606)--------: org.Hs.eg.db
# Mouse (10090)-------: org.Mm.eg.db
# Fruit Fly (7227)----: org.Dm.eg.db
# Rhesus monkey (9544): org.Mmu.eg.db
# Rat (10116)---------: org.Rn.eg.db
# Worm (6239)---------: org.Ce.eg.db
# Chimpanzee (9598)---: org.Pt.eg.db
# Zebrafish (7955)----: org.Dr.eg.db
if ( ! require("pak", quietly = TRUE)) install.packages('pak')
pak::pkg_install(c(
"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"
))
## Optional: add gene descriptions to exported tables, install annotables:
# available only for: human, mouse, rat, worm, fruit fly, Rhesus Monkey
if ( ! require("pak", quietly = TRUE)) install.packages('pak')
pak::pkg_install('stephenturner/annotables')
```
# Running goatea: Shiny application
Simply install the package and its dependencies, then run the code below
in R.
Note that the goatea color scheme is easily customizable, have fun
creating your own theme!
Click the ‘?’ buttons and hover over UI elements for explanation in
tooltips.
``` r
library(goatea)
## customizable coloring
colors <- list(
main_bg = "#222222",
darker_bg = "#111111",
focus = "#32CD32",
hover = "#228B22",
border = "#555555",
text = "#FFFFFF"
)
## run the goatea Shiny application
shiny::shinyApp(
ui = goatea:::goatea_ui,
server = function(input, output, session) {
goatea:::goatea_server(
input, output, session,
css_colors = colors)
}
)
```
# Running goatea: automated analyses
See the [vignette](https://mauritsunkel.github.io/goatea/goatea.html)
for more details on automated scripted analyses.
# GOAT reference
Koopmans, F. GOAT: efficient and robust identification of gene set
enrichment. Commun Biol 7, 744 (2024).
<https://doi.org/10.1038/s42003-024-06454-5>
# Contact
A thank you for your time and effort in using goatea, I hope it may aid
you in exploring your data!
For issues: <https://github.com/mauritsunkel/goatea/issues>
To collaborate, pull request or email me: <mauritsunkel@gmail.com>
# FAQ
Why does my file not download? \* For PPI: check if the string database
website is online. \* Generally: make sure you have read/write
permissions in the set base folder.
