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README.md

shinyGEO

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.

Official Website

http://gdancik.github.io/shinyGEO/

The preferred way of running shinyGEO locally is through docker:

  1. Download docker from https://www.docker.com/get-started

  2. Pull the docker image by running the following from your terminal:

    docker pull gdancik/shinygeo

  3. Run shinyGEO by using the command:

    docker run -it --rm -p 3838:3838 gdancik/shinygeo

  4. View shinyGEO by opening a web browser and entering localhost:3838 into the address bar.

Contributors

  • Main contributors: Jasmine Dumas, Michael Gargano, Garrett M. Dancik, PhD
  • Additional contributors: Ken-Heng Liao, Gregory Harper, Brandon Spratt

Acknowledgements

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.