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Genotyping ID using Shiny and Twitter Bootstrap to genotype using SSR's and Poppr for Phytophthora

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Genotype-ID

Creation of a Shiny server to develop population genetic tool ocurred to us while working on [poppr] (https://github.com/poppr/poppr) on the winter of 2013.

The goals of the Genotype-ID are

  • To create an easy framework for the reconstruction and identification on SSR data
  • To use [poppr] (https://github.com/poppr/poppr) in a highly efficient way, in order to create web-apps for biologists/researchers everywhere
  • To generate a genotyping webpage for species of Phytopthora

Species implemented so far

  • Phytophthora ramorum

Installation

Genotype-ID is based on R, it uses:

After installing the requirements, be sure that you have a folder named shiny-server on /var/. Download the files into /var/shiny-server/ using git pull:

$ git pull https://github.com/Tabima/Genotype-ID/

After downloading the files, start the shiny-server

$ sudo shiny-server &

App Deployment

And go to your preferred browser (Genotype-ID is known to have issues with Internet Explorer, so we recommend using Google Chrome or, better yet, Firefox) and go to the server port address:

http://localhost:3838/

The browser will show you a link to a folder called "Genotype-ID/", if you click on it, the application will deploy on shiny server and voila! there is your web-app.

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Genotyping ID using Shiny and Twitter Bootstrap to genotype using SSR's and Poppr for Phytophthora

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