GEOquery

The bridge between the NCBI Gene Expression Omnibus (GEO) and Bioconductor.

GEOquery downloads and parses data from the NCBI Gene Expression Omnibus — a public repository of high-throughput functional genomics data — into Bioconductor objects, so you can go from a GEO accession to an analysis-ready object in one call.

Capabilities

• Series, Samples, Platforms, DataSets. Parse any GEO entity (GSE, GSM, GPL, GDS) from either the compact Series Matrix or the full SOFT format.
• Modern object model. GSE Series Matrix records return SummarizedExperiment objects by default (or ExpressionSet via returnType = "ExpressionSet").
• RNA-seq. Retrieve NCBI's uniformly-computed RNA-seq quantifications with getRNASeqData().
• Single-cell. Inventory, group, and load single-cell supplementary data (10x Matrix Market, 10x HDF5, AnnData .h5ad, Seurat .rds) into SingleCellExperiment (or Seurat) objects, with each sample's GEO characteristics carried into colData.
• Supplementary files. List and download any attached files with getGEOSuppFiles().
• Search. Query GEO programmatically with searchGEO().
• Robust downloads. Streaming downloads with retries, an optional persistent BiocFileCache cache, and typed error conditions for tryCatch().

Installation

# from Bioconductor (recommended)
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("GEOquery")

# or the development version from GitHub
BiocManager::install("seandavi/GEOquery")

Quick start

library(GEOquery)

# A GSE via the fast Series Matrix path -> a list of SummarizedExperiment,
# one per platform.
gse <- getGEO("GSE2553")
se <- gse[[1]]
assay(se)      # expression matrix
colData(se)    # sample metadata
rowData(se)    # feature annotation

# Other entity types parse to GEOquery's S4 classes:
getGEO("GSM11805")   # a sample
getGEO("GPL96")      # a platform
getGEO("GDS507")     # a curated dataset

# See what supplementary files a study has, without downloading:
getGEOSuppFiles("GSE63137", fetch_files = FALSE)

Documentation

Six vignettes take you from first contact to downstream analysis — a quick-start plus in-depth articles covering the why and the workflows:

• Getting started
• Understanding GEO data formats
• Finding and downloading data
• RNA-seq quantifications
• Single-cell data from GEO
• From GEO to downstream analysis

Bioconductor landing pages: release · devel

Getting help

• Usage questions: the Bioconductor support site, tagged geoquery.
• Bugs and feature requests: the issue tracker — please include a GEO accession and sessionInfo().

Contributing

Contributions are welcome as pull requests or issues. See CONTRIBUTING.md for the development workflow, and follow the Bioconductor coding standards where possible.

Citation

If you use GEOquery, please cite:

Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics. 2007;23(14):1846–1847.

citation("GEOquery")