Local CeNGENApp use

If you are using the app intensively, or if you want to customize it, you can download the code from the Github repository along with the dataset (200 MB) and run them on a local R Shiny instance.

Step by step (full App)

First, you need to install a recent version of R and RStudio (recommended). Launch RStudio, and select “File > New Project”. In the pop-up window, choose “Version Control”, then “Git”. Enter the repository address:


and select where on your computer to create the directory. Then click “Create Project”, you should arrive in a new RStudio session. In the R console, copy/paste this command and press enter:


This should download the dataset, it may take a few minutes. Place it in the app directory. You then need to uncompress it:


If the uncompression worked, you can safely delete the .tar.gz file.

Then you need to install all the dependencies (R packages that are required for this app to run). In the R console, copy/paste these three commands:

required_packages <- c("BiocManager",
                        "shiny", "shinyjs", "shinythemes", "shinybusy",
                        "DT", "tidyverse", "pheatmap","ggridges", "cowplot",
                        "plotly","expss", "xlsx", "qs")


BiocManager::install(c("limma", "edgeR"))

and make sure the process concludes without errors. Note: you may need to close any other open RStudio window.

Create a blank file called google-analytics-script2.html:


Finally if all steps were successful, you should be able to start the App with this command:


or click on the “Run App” button on the top right of the RStudio window.


On older versions of R (<4.0), some functionalities may not work as expected.

Older versions of the dataset are available upon request: 1 May 2021, 15 June 2021, 6 July 2021, 220926.

The legacy app can be installed following instructions here: https://www.cengen.org/local-cengenapp-use