shinyGEO: a web-based application for performing differential expression and survival analysis on Gene Expression Omnibus datasets

Summary

Analyzing gene expression and correlating phenotypic data is an important method to discover insights about disease outcomes and prognosis. There are currently several web-based tools designed to address these analyses but are limited in usability, data pipeline access, and reproducibility. We describe an R Shiny web application, shinyGEO, that can download gene expression data sets directly from the Gene Expression Omnibus, and perform differential expression and survival analysis across selected genes and probes.

Citation

Dumas J, Gargano MA, Dancik GM. shinyGEO: a web-based application for analyzing Gene Expression Omnibus datasets. Bioinformatics. 2016 Dec 1;32(23):3679-3681 (link)

Running shinyGEO

For optimal performance, we recommend running shinyGEO locally by following the instructions at https://github.com/gdancik/shinyGEO

shinyGEO can also be run from the following sites:

Interested in contributing to shinyGEO? Source code and local installation instructions are available from github: https://github.com/gdancik/shinyGEO

Feedback

We love hearing from shinyGEO users. If you have questions, comments, or feature requests, please contact Garrett Dancik,

About

shinyGEO is a project of the Bioinformatics Laboratory at Eastern Connecticut State University. *, Computer Science major, Eastern Connecticut State University

Funding

This work was supported, in part, by Google Summer of Code funding to Jasmine Dumas in 2015.