GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation
BackgroundOver the past three decades there have been numerous molecular biology developments that have led to an explosion in the number of gene expression studies being performed. Many of these gene expression studies publish their data to the public database GEO, making them freely available. By analysing gene expression datasets, researchers can identify genes that are differentially expressed between two groups. This can provide insights that lead to the development of new tests and treatments for diseases. Despite the wide availability of gene expression datasets, analysing them is difficult for several reasons. These reasons include the fact that most methods for performing gene expression analysis require programming proficiency. ResultsWe developed the GEOexplorer software package to overcome several of the difficulties in performing gene expression analysis. GEOexplorer was therefore developed as a web application, that can perform interactive and reproducible microarray gene expression analysis, while producing a wealth of interactive visualisations to facilitate result exploration. GEOexplorer is implemented in R using the Shiny framework and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of exploratory data analysis and differential gene expression analysis intuitively and generate a broad spectrum of publication ready outputs. ConclusionGEOexplorer is distributed as an R package in the Bioconductor project (http://bioconductor.org/packages/GEOexplorer/). GEOexplorer provides a solution for performing interactive and reproducible analyses of microarray gene expression data, empowering life scientists to perform exploratory data analysis and differential gene expression analysis on GEO microarray datasets.