gSWITCH

gSWITCH is a tool for the identification and visualisation of ‘switch’ genes during the progression of cell-lineage stages or environmental-variable-dependent changes in cellular responses.

Data type: Bulk RNA-seq or single-cell RNA-seq data aggregated as pseudobulk.

Run gSWITCH with Docker

Docker is the recommended option for users who want to run gSWITCH without installing R, RStudio, or the required R packages.

Requirements

Install Docker Desktop and make sure Docker Desktop is running.

Apple silicon Mac

For a Mac with an M1, M2, M3, M4, or later Apple processor, open Terminal and download the gSWITCH image using:

docker pull --platform linux/amd64 ghcr.io/tanay-math/gswitch:1.0.0

Run gSWITCH using:

docker run --rm --platform linux/amd64 -p 3838:3838 ghcr.io/tanay-math/gswitch:1.0.0

Intel Mac, Windows, or Linux computer

Open Terminal or PowerShell and download the gSWITCH image using:

docker pull ghcr.io/tanay-math/gswitch:1.0.0

Run gSWITCH using:

docker run --rm -p 3838:3838 ghcr.io/tanay-math/gswitch:1.0.0

Open gSWITCH

Keep the Terminal or PowerShell window open.

Open a web browser and go to:

http://localhost:3838

To stop gSWITCH, return to the Terminal or PowerShell window and press:

Control + C

The Docker image needs to be downloaded only once. Run the docker pull command again when a newer version of gSWITCH is released.

Run gSWITCH directly in R

1. Clone the repository

Using Git:

git clone https://github.com/Tanay-math/gSWITCH.git

Move into the project folder:

cd gSWITCH

Alternatively, click Code → Download ZIP on the GitHub repository page, unzip the downloaded file, and open the resulting gSWITCH folder.

2. Open the project in RStudio

Open RStudio and set the working directory to the downloaded or cloned gSWITCH folder.

For example:

setwd("/path/to/gSWITCH")

3. Restore the R environment

Install renv if necessary:

install.packages("renv")

Restore the package versions recorded in renv.lock:

renv::restore()

4. Run gSWITCH

shiny::runApp()

The application should open in a web browser.

Troubleshooting MonoInc installation

MonoInc is required by gSWITCH and should be installed automatically by renv::restore().

If MonoInc is still missing, try:

install.packages("remotes")
remotes::install_version("MonoInc", version = "1.1")

Tutorial

A step-by-step tutorial is available in the Tutorial folder.

Example data

Example input data are available in the Example_data folder.

Citation

Ghosh T, Baror R, Zhao C, Sharma A, Au WH, Lakatos A, Goldman N, Franklin RJM (2026). The transcription factor BCL11A restores differentiation potential to aged oligodendrocyte progenitor cells. eLife 15:RP110038. https://doi.org/10.7554/eLife.110038.1

License

gSWITCH is available under the MIT License.

Contact

Dr Tanay Ghosh
tg369@cantab.ac.uk
writetotanay@gmail.com