Gene Expression Omnibus Analysis with Shiny 🔬
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README.md

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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/

How to install this package?

Install the development version from Github:

library(devtools)
install_github("jasdumas/shinyGEO")
library(shinyGEO)

How to use this package?

Update the series and platform meta-data:

shinyGEO::updateGEOdata()

Launch the shiny application locally:

shinyGEO::runshinyGEO()

Or launch the shiny application in a web browser:

http://bioinformatics.easternct.edu/shinyGEO/

Contributors

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

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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.

Learn more

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  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for shinyGEO in R doing r citation(package = 'shinyGEO')