WGCNA Online

An online application that lets users perform weighted gene co-expression network analysis on their data –
a no-code solution that helps you quickly get started and explore.

This project aims to create a GUI interface to the R WGCNA package.

Live version

A hosted version is available on shinyapps.io. Note that it is resource-limited.
The app sleeps to save resources when idle, leading to longer startup times. Please be patient.

Getting started

Prerequisites

R and git must be installed on your system.

Clone the repository

git clone https://github.com/Sciwhylab/WGCNA-Online.git
cd WGCNA-Online

Install required packages

In R, execute the following commands:

install.packages(c("shiny", "shinyWidgets", "stats", "bslib", "BiocManager", "DT", "here", "readr", "readxl"))

BiocManager::install(c("WGCNA", "impute", "flashClust"))

If you are having trouble with the above steps, refer to this answer on StackOverflow.

Run the Shiny App

First clone the repository.
Then, go to the project root and execute the following in R.

shiny::runApp(, host = "0.0.0.0")

Using the Dockerfile

If you have Docker installed, you can build, run and deploy the app using the provided Dockerfile.

You can build the image using the following command:

docker build -t wgcna-online .

And run the container using: (replace 8080 with the port you want to use)

docker run --name "wgcna" --rm -p 8080:3838 wgcna-online

Visit http://localhost:8080 to access the app.
If you are using a server, replace localhost with the server's IP address.

Troubleshooting

If you are facing package installation problems while deploying the app to shinyapps.io, execute the following in R.

options(repos = c(getOption("repos"),  BiocManager::repositories()))