shinyGEO is a web-based tool that allows a user to download the expression and sample data from a Gene Expression Omnibus dataset, select a gene of interest, and perform a survival or differential expression analysis using the available data. For both analyses, shinyGEO produces publication-ready graphics and generates R code ensuring that all analyses are reproducible. The tool is developed using shiny, a web application framework for R, a language for statistical computing and graphics.

Shinyapps.io: https://jasminedumas.shinyapps.io/shinyGEO

GitHub Repo Page: http://github.com/jasdumas/shinyGEO/

Github Homepage: http://jasdumas.github.io/shinyGEO/

Eastern CT Primary App Hosting: http://bioinformatics.easternct.edu/shinyGEO/

1. Download R from https://cran.r-project.org

2. From within R, install 'shiny' by typing install.packages("shiny")

3. Type the following from within R: runGitHub("shinyGEO", "jasdumas")

Main contributors: Jasmine Dumas, Michael Gargano, Garrett M. Dancik, PhD

Additional contributors: Ken-Heng Liao, Gregory Harper, Brandon Spratt

This work was supported, in part, by Google Summer of Code funding to JD in 2015. MG, KHL, GH, and BS contributed as part of an independent study in Computer Science / Bioinformatics while undergraduate students at Eastern Connecticut State University, Willimantic, CT, USA.

Feel free to check out the project wiki

25 AUGUST 2015: The current (post-GSoC version) development version as of 21 August 2015 19:00 UTC to the present can be found here as per the program code submission guidelines and the submitted GSoC release can be found here.

11 SEPTEMBER 2015: This GitHub Repo and corresponding links have be updated to a new name to conform with CRAN naming conventions and for deployment guidelines

2 OCTOBER 2015: The application has been deployed to shinyapps.io cloud service at https://jasminedumas.shinyapps.io/shinyGEO Report bugs, glitches, and general comments as this is the first release designated for testing and configuration.

7 JANUARY 2016: The application will also be deployed on the Eastern CT State University Shiny Server

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Jasmine Dumas @jasdumas / @shiny_GEO