GEOquery

This is the released version of GEOquery; for the devel version, see GEOquery.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-8991-6458

Maintainer: Sean Davis <seandavi at gmail.com>

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

Sean Davis. GEOquery: Get data from NCBI Gene Expression Omnibus (GEO). doi:10.18129/B9.bioc.GEOquery, R package version 2.80.0, https://bioconductor.org/packages/GEOquery.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOquery")

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

Documentation

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

browseVignettes("GEOquery")

GEOquery.html	HTML	R Script
single-cell.html	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel
Version	2.80.0
In Bioconductor since	BioC 1.8 (R-2.3) (20.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), methods, Biobase
Imports	readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2
System Requirements
URL	https://github.com/seandavi/GEOquery http://seandavi.github.io/GEOquery http://seandavi.github.io/GEOquery/
Bug Reports	https://github.com/seandavi/GEOquery/issues/new

Suggests	knitr, rmarkdown, BiocGenerics, testthat, covr, markdown, quarto, DropletUtils, SingleCellExperiment
Linking To
Enhances
Depends On Me	DrugVsDisease, dyebiasexamples, GSE103322, GSE13015, GSE62944, SCAN.UPC
Imports Me	BeadArrayUseCases, bigmelon, BioPlex, ChIPXpress, COTAN, DExMA, EGAD, geneExpressionFromGEO, GEOexplorer, GSE13015, healthyControlsPresenceChecker, minfi, Moonlight2R, MoonlightR, phantasus, RCPA, recount
Suggests Me	airway, AnnoProbe, antiProfilesData, ath1121501frmavecs, AUCell, autonomics, BED, CimpleG, ctsGE, dearseq, diffcoexp, dyebias, easybio, EpiDISH, EpiMix, epiSeeker, fdrci, fgsea, FLAMES, GeneExpressionSignature, GenomicOZone, GeoTcgaData, maGUI, metaMA, methylclock, MLML2R, multiClust, MultiDataSet, muscData, NACHO, omicsPrint, PCAtools, phantasusLite, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, quantiseqr, RegEnrich, RegParallel, RFGeneRank, RGSEA, Rnits, scregclust, skewr, spatialHeatmap, TargetScore, TcGSA, tinyarray, zFPKM
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GEOquery_2.80.0.tar.gz
Windows Binary (x86_64)	GEOquery_2.80.0.zip
macOS Binary (big-sur-x86_64)	GEOquery_2.80.0.tgz
macOS Binary (sonoma-arm64)	GEOquery_2.80.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GEOquery
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GEOquery
Package Short Url	https://bioconductor.org/packages/GEOquery/
Package Downloads Report	Download Stats