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GEOquery specifications


Unique identifier OMICS_01972
Name GEOquery
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.48.0
Stability Stable
limma, methods, BiocGenerics, Biobase, testthat, dplyr, rmarkdown, knitr, readr, httr, xml2, tidyr, magrittr, covr
Maintained Yes


No version available


Publication for GEOquery

GEOquery citations


Identification of potential pathogenic genes associated with osteoporosis

PMCID: 5935809
PMID: 29203636
DOI: 10.1302/2046-3758.612.BJR-2017-0102.R1

[…] The two microarray data sets ( and were downloaded using the GEOquery package with R version (The R Foundation for Statistical Computing, Vienna, Austria) from the Gene Expression Omnibus (GEO) database. These two microarray data sets were from the blood sample […]


CXCL9/10/11, a regulator of PD L1 expression in gastric cancer

BMC Cancer
PMCID: 5916585
PMID: 29690901
DOI: 10.1186/s12885-018-4384-8

[…] om the Korean patient cohort [].The TCGA data was preprocessed according to the Bioconductor/TCGABiolinks function package flow. The gene expression profile data were extracted using the Bioconductor/GEOquery function package. Gene CD274 corresponds to two probes, “223834_at” and “227458_at”, and subsequent analysis was performed on the above two probes. The expression of CD274 in the samples was […]


Curated compendium of human transcriptional biomarker data

Sci Data
PMCID: 5903354
PMID: 29664470
DOI: 10.1038/sdata.2018.66
call_split See protocol

[…] For each dataset, we wrote custom R scripts that download, parse, and reformat the clinical annotations. Initially, these scripts retrieve data from GEO using the GEOquery package. Next they generate a tab-delimited text file for each dataset that contains all available clinical annotations, except those with identical values for all samples (for example, platf […]


A meta analysis of public microarray data identifies biological regulatory networks in Parkinson’s disease

BMC Med Genomics
PMCID: 5899355
PMID: 29653596
DOI: 10.1186/s12920-018-0357-7

[…] GEO2R is an interactive web tool that is based on GEOquery and limma R packages from the Bioconductor project that is used to identify DEGs by comparing different groups of GEO Series samples []. In this study, each individual dataset was processed u […]


The constitutive differential transcriptome of a brain circuit for vocal learning

BMC Genomics
PMCID: 5883274
PMID: 29614959
DOI: 10.1186/s12864-018-4578-0
call_split See protocol

[…] solation, oligo array hybridizations, gene expression normalization, and partial outcomes are available for nXIIts [], RA [], and Area X []. For our present analysis of these oligo arrays we used the GEOquery and limma R packages (NCBI Gene Expression Omnibus; [] with the Benjamini & Hochberg false discovery rate method to identify differentially expressed oligos from the user-supplied normalized […]


Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy

PLoS One
PMCID: 5846794
PMID: 29529088
DOI: 10.1371/journal.pone.0194225
call_split See protocol

[…] The datasets GSE1004 and GDS3027 were downloaded from NCBI GEO using the R Bioconductor package GEOquery. Dataset GSE1004 was obtained measuring RNA expression in quadriceps biopsies and it includes 12 DMD patients and 12 controls. The DMD biopsies were from young (5- to 7-year-old) males showin […]


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GEOquery institution(s)
Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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