How to create a multiModel OmicNavigator study

This repository contains an example of how to use the OmicNavigator R package to convert a publicly available multi-model omic analysis into a study package to be explored with the OmicNavigator app. For more details, please see the User's Guide attached to the latest release.

Files:

• setup.R - Installs the required R packages for the example

• data/ - The input differential expression data (excel file) as downloaded from article "The Global Phosphorylation Landscape of SARS-CoV-2 Infection", published in CELL, Vol. 182 (3), pages 685-712.e19. 2020.

• build.R - Builds the OmicNavigator study package from the data found in data/. Installs the study package and starts the web app.

Run the code

Follow the steps below to install the dependencies and create the OmicNavigator study package.

1. Install R package dependencies

   source("setup.R", local = new.env())
   

2. Generate the report in html format. The output file is exported to data/.

   library(rmarkdown)
   render("report.Rmd", output_file = "data/report.html", envir = new.env())
   

3. Create and install the OmicNavigator study package. This reads the analysis results files in data/, converts them to an OmicNavigator study package, installs the package, and starts the app.

   source("build.R")
   

Acknowledgements

The example was adapted from the article "The Global Phosphorylation Landscape of SARS-CoV-2 Infection", published in Cell, Vol. 182 (3), pages 685-712.e19. 2020.

If you use the data, please cite:

Bouhaddou M, Memon D, Meyer B, et al.: The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020; 182(3): 685-712.e19. https://www.sciencedirect.com/science/article/pii/S0092867420308114