The Celiac Microbiome Repository Web App

This is the R Shiny web application used to view the Celiac Microbiome Repository (CMR). The CMR is the best effort to comprehensively combine all high throughput sequencing datasets of the gut microbiome related to celiac disease.

View the live web app at www.celiac.shinyapps.io/celiac-webapp/

View the repository at www.github.com/CeliacMicrobiomeRepo/celiac-repository

Authors

• Haig Bishop (haigvbishop@gmail.com)
• Peter Prendergast

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Requirements & Licenses

Project License

This code for this project is licensed under the GNU General Public License v3.0 (GPL-3) to ensure compatibility.

R Dependencies

• shiny: GPL-3
• DT: GPL-3
• ggplot2: MIT (Code is MIT, package is GPL-3 due to dependencies)
• dplyr: MIT
• sf: GPL-2 | GPL-3 | MIT (Complex licensing, see CRAN page)
• rworldmap: GPL-2 | GPL-3 (See CRAN page)
• rworldxtra: GPL-2 | GPL-3 (See CRAN page)
• rnaturalearth: MIT
• rnaturalearthdata: CC0 1.0
• countrycode: GPL-3 (See CRAN page)
• gridExtra: GPL-2 | GPL-3 (See CRAN page)
• reshape2: MIT
• markdown: MIT
• stringr: MIT

Python Dependencies (for data fetching)

• requests: Apache 2.0

JavaScript Dependencies

• jQuery: MIT

Deployment

1. Your system needs R some R packages
   • R 4.4.1 is proven to be stable
   • Use install_deps.R to see R packages
2. You'll need to obtain the .tsv data files and latest_version.json from the CMR
   • The Python script fetch_repo_data.py does this automatically.
   • The 4 .tsv files and latest_version.json sit in repo_data
3. To deploy the application to shinyapps.io run this (or deploy.R) in R:

library(rsconnect)
rsconnect::deployApp(
  appDir = "/home/haig/Repos/celiac-webapp",
  account = "celiac"
)