Gene Feature Plot App

An interactive Shiny app for visualizing gene expression from Seurat RDS objects.
Select genes, dimensionality reductions, and assays to generate customizable feature and dot plots for single-cell data analysis.

Features

• Upload Seurat .RDS objects (up to 1GB).
• Select and visualize specific genes using feature and dot plots.
• Dynamically choose reductions (e.g., PCA, UMAP, t-SNE) and assays (e.g., RNA, ADT, ATAC) directly from the loaded object.
• Download high-resolution plots in TIFF format.
• Robust error handling for invalid gene names, missing reductions, and file issues.

Requirements

• R version ≥ 4.0
• R packages:
  • shiny
  • Seurat
  • cowplot
  • ggplot2

Install required packages with:

install.packages(c("shiny", "cowplot", "ggplot2"))
if (!requireNamespace("Seurat", quietly = TRUE)) {
  install.packages("Seurat")
}

Usage

1. Clone the repository

git clone https://github.com/yourusername/gene-feature-plot-app.git
cd gene-feature-plot-app

2. Run the app in R

library(shiny)
runApp()

3. Using the app:

• Upload a Seurat .RDS object
• Select your desired reduction and assay
• Enter the gene name to visualize
• View and download the generated plots

Contributing

Contributions are welcome!

License

This project is provided as is.
Feel free to use and modify this code for personal or educational purposes.
For commercial use or redistribution, please contact the author.