Interactive exploration and visualization of USQ bladder cancer cohort data

usqExplore is an R Shiny application designed for dynamic analysis and visualization of USQ cohort metadata, gene expression, and molecular subtype information. The app enables users to filter samples, generate heatmaps, perform survival analyses, and explore clinical endpoints, supporting reproducible and insightful workflows in bladder cancer research.

usqExplore

Welcome to the UROSCANSEQ Explorer Shiny App!

What does the app do?

UROSCANSEQ Explorer is an interactive Shiny application for exploring gene expression, clinical metadata, and survival analysis in urothelial cancer. The app provides:

• Dynamic heatmaps of gene expression and meta-genes
• Interactive filtering and annotation of samples by clinical and molecular features
• Survival analysis (Kaplan-Meier plots) by gene, meta-gene, or LundTax signature
• Forest plots of hazard ratios for LundTax signatures using Cox models
• Downloadable sample lists and tables

How to Download and Run Locally

Step-by-step guide

1. Clone the Repository Clone the repository to your local machine:

git clone https://github.com/mattssca/usqUtils.git

2. Download data

   • Log in to LU Box and locate the associated data folder for this package (/Git/data/usqExplore).
   • Download the contents of the LU Box data folder.
   • Add the folder (with its contents) to the cloned version of usqExplore's data fodler usqExplore/data/

3. Install required R packages In the RStudio Console, run:

   install.packages(c("shiny", "plotly", "bslib", "DT", "shinyWidgets", "RColorBrewer", "pheatmap", "later", "colourpicker", "survival", "survminer"))

4. Run the app

   • Set your working directory to the cloned repo.
   • In the RStudio Console, run:

     shiny::runApp('app.R')

   • The app will open in your web browser

Need help?

If you have any issues or questions, please open an issue on GitHub or contact the maintainer.

Enjoy exploring your data!