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.
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)
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