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README.md

WIlsON: Webbased Interactive Omics visualizatioN - Applications

Abstract

This repository contains reference applications that utilize functions from the WIlsON R package. It is primarily intended to empower high-throughput service platforms to offer access to pre-calculated high-throughput screening results to non-computational scientist. Facilitated by an open file format, WIlsON supports all types of -omics screens, serves results via a web-based dashboard, and enables users to perform analyses and generate publication-ready visualizations without programming skills.

Application deployment

A WIlsON application typically consists of the following components:

  • an app.R file, containing all R code of the application.
  • a data directory, containing input file(s) in CLARION format.
  • an introduction directory, containing markdown documents of the landing page.
  • a www directory, containing images and logos.

Applications described here can easily be deployed locally, on a centralized R Shiny server, or anywhere using Docker containers:

Using RStudio

  1. On Windows-based systems, install RTools.
  2. Install all prerequisites using install.packages("BiocManager", "webshot"); BiocManager::install(c("shinyBS", "shinydashboard", "shinythemes", "htmltools", "wilson")).
  3. Download the WIlsON applications from the Releases page and extract them on your local disk.
  4. Set the working directory to the extracted release using setwd("file/to/extracted_release").
  5. Run an app, e.g. shiny::runApp("wilson-basic/").

Using a Shiny server

  1. Similar to the local usage, install all prerequisites using install.packages("BiocManager", "webshot"); BiocManager::install(c("shinyBS", "shinydashboard", "shinythemes", "htmltools", "wilson")).
  2. Download the WIlsON applications from the Releases page and extract them on the shiny servers disk.
  3. Move the application folder(s) into the shiny servers application folder (e.g. to /srv/shiny-server/wilson-basic).
  4. Restart your shiny server.

Using Docker Containers

  1. Pull one of WIlsONs application images using e.g. docker pull loosolab/wilson-basic:2.1.0.
  2. Rund the application image using docker run -d loosolab/wilson-basic:2.1.0.

Available images

Currently, the following application images are available:

Loading custom data

For deployments using (RStudio)[#using-rstudio] and Shiny Server, it is sufficient to add CLARION files to the /data folder and reload the app/server. The new dataset can be selected from the within the app, using the drop down menu in the feature selection panel.

For the Docker deployment, mount a directory with the CLARION files to srv/shiny-server/external_data/ using Dockers -v /path/to/files:/srv/shiny-server/external_data.

How to cite

Further information

License

This project is licensed under the MIT license.

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