GEOquery

GEOquery is an R package from Bioconductor that provides programmatic access to the NCBI Gene Expression Omnibus (GEO). It enables researchers to retrieve GEO series (GSE), platforms (GPL), and samples (GSM), as well as associated metadata and supplementary files, directly from within R. The package is designed to support reproducible data analysis workflows by converting downloaded data into R data structures suitable for downstream analysis.

Core functionality includes the getGEO function, which downloads GEO data and typically returns an ExpressionSet or a list of ExpressionSet objects when multiple series are requested, optionally including processed data matrices. It can fetch data in several formats, such as Series Matrix, SOFT, and MINiML, and it can also retrieve supplementary files for a series via getGEOSuppFiles. The package handles metadata extraction, including platform annotations and sample characteristics, allowing mapping of probe IDs to gene identifiers.

Output and interoperability: GEOquery objects integrate with Bioconductor data classes, including ExpressionSet and SummarizedExperiment, enabling downstream analysis with limma, edgeR, or other packages. The tool works in concert with GEOmetadb for fast local access to GEO metadata, and it follows Bioconductor conventions for package maintenance and documentation.

Usage note: Retrieval can be bandwidth- and time-intensive for large series, and some GEO data may require multiple requests or extra parsing steps. Users should ensure compatible R and Bioconductor versions and consider caching results to reduce network load.

See also: Gene Expression Omnibus, GEOmetadb, Bioconductor, ExpressionSet, SummarizedExperiment.