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GEOquery | A bridge between the Gene Expression Omnibus (GEO) and BioConductor


A package that allows access to the wealth of information within GEO directly from BioConductor, eliminating many formatting and parsing problems that have made such analyses labor-intensive in the past. The primary goal of GEOquery is to download and parse the SOFT format files from GEO, maintaining all of the information contained in the GEO records. The design of GEOquery makes accessing data from GEO very simple. There is only one command that is needed, getGEO. GEOquery provides a bridge between the BioConductor analysis tools and the vast public data resources contained in the NCBI GEO repositories. By maintaining the full richness of the GEO data rather than focusing on getting only the ‘numbers’, it is possible to integrate GEO data into Bioconductor data structures and to perform analyses on that data quite quickly and easily or to export the data into any number of formats for use by other tools or for local storage and data mining.

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GEOquery classification

GEOquery specifications

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Command line interface
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Unix/Linux, Mac OS, Windows
GNU General Public License version 2.0
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GEOquery distribution


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GEOquery support



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Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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