ScanGEO: parallel mining of high-throughput gene expression data

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Current options to mine publicly available gene expression data deposited in NCBI's gene expression omnibus (GEO), such as the GEO web portal and related applications, are optimized to reanalyze a single study, or search for a single gene, and therefore require manual intervention to reanalyze multiple studies for user-specified gene sets. ScanGEO is a simple, user-friendly Shiny web application designed to identify differentially expressed genes across all GEO studies matching user-specified criteria, for a flexible set of genes, visualize results and provide summary statistics and other reports using a single command.

Availability and implementation

The ScanGEO source code is written in R and implemented as a Shiny app that can be freely accessed at For users who would like to run a local instantiation of the app, the R source code is available under a GNU GPLv3 license at


Supplementary information

Supplementary data are available at Bioinformatics online.

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