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Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: Release (3.19)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Author: Sean Davis [aut, cre]

Maintainer: Sean Davis <seandavi at>

Citation (from within R, enter citation("GEOquery")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using GEOquery HTML R Script
Reference Manual PDF


biocViews DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel
Version 2.72.0
In Bioconductor since BioC 1.8 (R-2.3) (18 years)
License MIT
Depends methods, Biobase
Imports readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, R.utils
System Requirements
Bug Reports
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Suggests knitr, rmarkdown, BiocGenerics, testthat, covr, markdown
Linking To
Depends On Me DrugVsDisease, SCAN.UPC, dyebiasexamples, GSE103322, GSE13015, GSE62944
Imports Me bigmelon, ChIPXpress, crossmeta, DExMA, EGAD, GEOexplorer, minfi, Moonlight2R, MoonlightR, phantasus, recount, SRAdb, BeadArrayUseCases, BioPlex, GSE13015, healthyControlsPresenceChecker, easyDifferentialGeneCoexpression, geneExpressionFromGEO, MetaIntegrator, RCPA, seeker
Suggests Me AUCell, autonomics, CBNplot, COTAN, ctsGE, dearseq, debCAM, diffcoexp, dyebias, EpiDISH, EpiMix, fgsea, FLAMES, GeneExpressionSignature, GenomicOZone, GeoTcgaData, methylclock, multiClust, MultiDataSet, omicsPrint, PCAtools, phantasusLite, quantiseqr, RegEnrich, RGSEA, Rnits, runibic, skewr, spatialHeatmap, TargetScore, zFPKM, ath1121501frmavecs, airway, antiProfilesData, muscData, parathyroidSE, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, RegParallel, AnnoProbe, BED, fdrci, maGUI, metaMA, MLML2R, NACHO, TcGSA, tinyarray
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GEOquery_2.72.0.tar.gz
Windows Binary
macOS Binary (x86_64) GEOquery_2.72.0.tgz
macOS Binary (arm64) GEOquery_2.72.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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