The singleCellComic Game: An Interactive scRNA-seq Adventure

Welcome to the singleCellComic Game! This is an interactive Shiny application designed to teach the fundamental concepts of single-cell RNA sequencing (scRNA-seq) analysis through a fun, story-driven, and visual narrative.

The Concept

The core idea of this game is to make abstract scRNA-seq data intuitive and memorable. We do this by translating complex concepts into a "Cell Comic" analogy:

• Gene Expression is represented by a cell's visual features (e.g., moustache size, hair style, headphones).
• Cell Types are unique characters defined by a combination of these features.
• Bioinformatics Analyses are steps in a 4-act story where you help solve a biological mystery.

This gamified approach guides users through a standard analysis workflow, explaining the why behind each step, from basic clustering to discovering novel cell subtypes.

The Story in 4 Acts

The game is structured as a narrative journey:

• Act 1: A Peaceful World - Learn the basics of UMAP visualization and gene expression in a perfect, single-batch dataset.
• Act 2: The Viral Invasion - Encounter the critical problem of batch effects when combining data from two different sources and use the Harmony algorithm to solve it.
• Act 3: The Reinforcements - Use your corrected dataset as a reference to identify unknown cells using label transfer.
• Act 4: The Lost Labels - Perform unsupervised clustering to discover cell types from scratch and uncover hidden biological subtypes.

Key Concepts Taught

• Dimensionality Reduction (UMAP)
• Visualizing Gene Expression (FeaturePlots, VlnPlots)
• Batch Effects
• Data Integration with Harmony
• Label Transfer / Reference Mapping
• Unsupervised Clustering
• Cluster Annotation & Subtype Discovery

Technology Stack

This application is built entirely in R and powered by:

• Shiny: For the interactive web framework.
• Seurat & Harmony: For the core scRNA-seq analysis and data integration.
• ggplot2 & patchwork: For all data visualizations and creating the "Cell Comic" characters.
• dplyr & purrr: For data manipulation.
• shinycssloaders: For loading indicators during computation.

How to Run the Game

Prerequisites

• R (version 4.0 or newer)
• RStudio IDE (recommended)

Installation

1. Clone the repository:

   git clone [URL-to-your-repository]
   cd [repository-folder]

2. Install Required R Packages: Excecute the install_packages.R script to install the required packages. Alternatively, you can install them by running the following command in the R console:

   install.packages(c("shiny", "shinycssloaders", "ggplot2", "dplyr", "patchwork", "Seurat", "harmony", "purrr", "tibble", "scales", "stringr", "ggforce", "circlize"))

3. File Structure: Ensure your directory is structured correctly. The application expects the image file to be in a www subdirectory.

   /your-app-folder
   ├── cell_comic_game.R
   ├── functions.R
   ├── install_packages.R
   ├── README.md
   ├── LICENSE
   ├── /cache
   └── /www
       └── header_logo.png
   

Launch the App

Open the cell_comic_game.R file in RStudio and click the "Run App" button in the top-right corner of the editor pane.

Contact

This game was developed by Fabian Wu.

For questions, feedback, or collaborations, please reach out at [email protected].