RNA-seq Differential Gene Expression Analysis App

Author: Eren Ada, PhD
Last Updated: October 21, 2025
Version: 1.0

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Overview

A comprehensive Shiny app that guides you through RNA-seq differential expression with DESeq2: upload data, build contrasts (with optional covariates), run analysis, review/export results, perform GO enrichment, and create publication-ready volcano plots. You can also use pre-computed DEG CSVs for Enrichment and Volcano without running DESeq2 in-app.

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Requirements

• R >= 4.1.0
• Use the installer to fetch CRAN/Bioconductor packages

source("install_packages.R")
# optional
source("check_packages.R")

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Installation & Run

git clone https://github.com/erenada/RNA_DEG_APP.git
cd RNA_DEG_APP

# Install dependencies once
source("install_packages.R")

# Launch the app
shiny::runApp()
# or
source("app.R")

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Quick Start (Essentials)

1. Data Input: upload count matrix and metadata; select organism and ID type; pass validation
2. Experimental Design: drag samples to Numerator/Denominator; optionally add covariates; create contrasts
3. DESeq2 Configuration: choose test (Wald/LRT), alpha, optional shrinkage; run analysis
4. Results: browse per-contrast tables; export all/significant genes
5. Enrichment (optional): run GO BP/MF/CC on significant genes; export tables and gene lists
6. Volcano: customize thresholds/labels/colors; export PDF/PNG and parameters

• Example datasets: example_data/ (toy and example CSVs)
• Outputs: written to browser and saved under results/ where applicable

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Screenshots

Volcano Plot Visualization

Interactive volcano plots with customizable thresholds, gene labeling, and publication-ready export options

Enrichment Analysis Results

GO enrichment analysis with interactive tables, bar plots, dot plots, and per-term gene list downloads

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Documentation

• Documentation index: documentation/README.md
• Quick Start Guide: documentation/quick_start_guide.md
• Tab Guides (in order):
  • Data Input: 01_data_input_tab.md
  • Experimental Design: 02_experimental_design_tab.md
  • DESeq2 Configuration: 03_analysis_configuration_tab.md
  • Results: 04_results_display_tab.md
  • Enrichment: 05_enrichment_tab.md
  • Volcano Plot: 06_volcano_tab.md

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Notes

• Organism databases (org.Mm.eg.db, org.Hs.eg.db) are loaded on demand from the Data Input tab.
• Pre-computed DEG CSVs can be used directly in Enrichment and Volcano tabs.

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License

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (see LICENSE).

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Contact / Support

Author: Eren Ada, PhD
Harvard Medical School, Department of Immunology
GitHub: @erenada

For questions:

• Using the app: see the tab guides and Quick Start
• Bugs/requests: open an issue on GitHub