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
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") install.packages(required_packages) 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
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