richStudio

R Shiny application for integrative functional enrichment analysis and visualization of multiple gene datasets.

Features

• Enrichment Analysis: Perform functional enrichment using GO, KEGG, and Reactome databases
• Multiple Clustering Methods: Choose from richR (Kappa), Hierarchical, or DAVID-style clustering
• Interactive Visualization: Bar plots, dot plots, heatmaps, and network graphs
• Session Save/Load: Save your analysis state and reload it later
• Multiple Species Support: 20+ supported organisms

Installation

Quick Start

# Install dependencies
source("install_dependencies.R")
install_all_dependencies()

# Or if you have the richCluster tarball locally:
install_all_dependencies("../richCluster_1.0.1.tar.gz")

# Load and run
devtools::load_all()
richStudio::launch_richStudio()

Using renv (Recommended for reproducibility)

renv::restore()
devtools::load_all()
richStudio::launch_richStudio()

Manual Installation

# CRAN packages (including richCluster)
install.packages(c("shiny", "shinydashboard", "shinyjs", "shinyWidgets",
                   "shinyjqui", "dplyr", "tidyverse", "ggplot2", "plotly",
                   "heatmaply", "DT", "jsonlite", "writexl", "zip", "richCluster"))

# Bioconductor packages (if needed)
BiocManager::install(c("AnnotationDbi", "org.Hs.eg.db"))

# GitHub packages
devtools::install_github("guokai8/richR")
devtools::install_github("guokai8/bioAnno")

Usage

Online Version

Visit: http://hurlab.med.und.edu:3838/richStudio

Local Development

# Load the package
devtools::load_all()

# Launch the application
richStudio::launch_richStudio()

As RStudio Project

1. Open richStudio.Rproj in RStudio
2. Run devtools::load_all()
3. Run richStudio::launch_richStudio()

Clustering Methods

richStudio v0.1.5 supports three clustering algorithms:

Method	Description	Best For
richR (Original)	Kappa-based clustering using gene overlap	Quick clustering with simple parameters
Hierarchical	Flexible clustering with multiple linkage methods	Fine-tuned control over clustering behavior
DAVID	DAVID-style functional clustering	Compatibility with DAVID results

Hierarchical Clustering Options

• Distance Metrics: Kappa (Cohen's Kappa), Jaccard
• Linkage Methods: Single, Complete, Average, Ward

App Overview

Upload Files

Upload DEG sets or enrichment results in various formats:

• .txt, .csv, .tsv files
• Text input (gene lists)

Enrichment

• Supported databases: GO, KEGG, Reactome
• Supported ontologies: BP (Biological Process), MF (Molecular Function), CC (Cellular Component)
• 20+ supported species

Clustering

1. Select enrichment results to cluster
2. Choose clustering method and parameters
3. View intermediate results (distance matrix, seeds)
4. Export clustered results

Visualization

• Bar plots: Enrichment significance
• Dot plots: Gene ratio visualization
• Heatmaps: Term-sample relationships
• Network plots: Term similarity networks
• Cluster heatmaps: Comprehensive and individual term views

Save/Load Session

• Save analysis state as RDS or JSON
• Reload sessions to continue analysis
• Export individual results (CSV, TSV, Excel)
• Export all results as ZIP archive

Project Structure

richStudio/
├── DESCRIPTION          # Package metadata
├── NAMESPACE            # Exported functions
├── R/                   # R source files
│   ├── rr_cluster.R     # Clustering functions
│   ├── cluster_tab.R    # Clustering UI/server
│   ├── enrich_tab.R     # Enrichment UI/server
│   ├── save_tab.R       # Save/load functionality
│   └── ...              # Other modules
├── inst/
│   ├── application/     # Shiny app entry point
│   │   └── app.R
│   └── extdata/         # Demo data
├── src/                 # C++ source (Rcpp)
├── tests/               # Unit tests
└── man/                 # Documentation

Development

Build Commands

# Restore dependencies
renv::restore()

# Compile C++ and load package
Rcpp::compileAttributes()
devtools::load_all()

# Run tests
devtools::test()

# Generate documentation
devtools::document()

# Full check
devtools::check()

Code Style

• tidyverse-style R (snake_case, <- assignment)
• 2-space indentation
• roxygen2 documentation for exported functions

Authors

• Junguk Hur - Lead developer, maintainer (hurlabshared@gmail.com)
• Sarah Hong - Core development
• Jane Kim - Contributions

License

GPL-3

Links

• Public Server: http://hurlab.med.und.edu:3838/richStudio
• Issues: https://github.com/hurlab/richStudio/issues
• richCluster Package: https://github.com/hurlab/richCluster