Shiny Workshop: Exploring Biological Data with R

This repository contains materials for a short course on building interactive web applications using Shiny in R. The goal of this workshop is to introduce the core concepts of Shiny and demonstrate how it can be used to explore biological datasets.

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Data

This workshop uses a simplified version of the airway RNA-seq dataset, a publicly available dataset from Bioconductor.

• The dataset contains gene expression measurements from human airway smooth muscle cells
• Samples include both treated (dexamethasone) and untreated conditions
• The original dataset has thousands of genes; for this workshop, it has been reduced to the 500 most variable genes to make exploration faster and more intuitive

The data is stored as a SummarizedExperiment object, a common Bioconductor data structure that keeps:

• expression data (counts)
• sample metadata (e.g., treatment group)
• gene metadata (e.g., gene identifiers)

File location:data/simple_airway_se.rds

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Shiny App

The app in this repository is a minimal example designed to illustrate the basic structure of a Shiny application.

What the app shows

• The number of samples in the dataset
• The number of genes in the dataset

Key Shiny concepts demonstrated

• User Interface (UI): what the user sees
• Server logic: how R processes and returns results
• Outputs: displaying results in the app

Run the app

Open app.R in RStudio and click Run App, or run:

shiny::runApp()

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Getting Started (Download the Repository)

To use these materials, you can download the repository: git clone https://github.com/NIH-CARD/R-Shiny-Bioinformatics-Training.git