ScanGEO: parallel mining of high-throughput gene expression data.

ABSTRACT: Summary: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 http://scangeo.dartmouth.edu/ScanGEO/. 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 https://github.com/StantonLabDartmouth/AppScanGEO. Contact:[e-mail]. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Koeppen K 

PROVIDER: S-EPMC5860173 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature