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 (570 MB) and run them on a local R Shiny instance.

Step by step

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:

https://github.com/cengenproject/CengenApp

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:

download.file("http://storage.cengen.org/Dataset_1May_2021.rda", "Dataset_1May_2021.rda")

This should download the dataset, it may take a few minutes.

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 two commands:

required_packages <- c("tidyverse", "BiocManager",
                        "DT", "expss", "Seurat",
                        "ggrepel", "ggridges", "cowplot",
                        "plotly", "pheatmap",
                        "shiny", "shinyjs", "shinythemes", "shinybusy",
                        "htmltools", "jsonlite")

install.packages(required_packages)

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

Open the file “ui.R” (click on it in the “Files” panel), and delete or comment out the line 56:

tags$head(includeHTML(("google-analytics-script2.html"))),

And save the modified script.

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

shiny::runApp(".")