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.
http://gdancik.github.io/shinyGEO/
Install the development version from Github:
library(devtools)
install_github("jasdumas/shinyGEO")
library(shinyGEO)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/
- 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.
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.
- Read the abstract about
shinyGEOpublished in Bioinformatics.
- Please report any issues or bugs.
- License: MIT
- Get citation information for
shinyGEOin R doingr citation(package = 'shinyGEO')