GEOquery

This is the development version of GEOquery; for the stable release version, see GEOquery.

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: Development (3.21)

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: )

Maintainer: Sean Davis <seandavi at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Using GEOquery	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel
Version	2.75.0
In Bioconductor since	BioC 1.8 (R-2.3) (18.5 years)
License	MIT + file LICENSE
Depends	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
Linking To
Enhances
Depends On Me	DrugVsDisease, SCAN.UPC, dyebiasexamples, GSE103322, GSE13015, GSE62944
Imports Me	ChIPXpress, DExMA, EGAD, GEOexplorer, Moonlight2R, MoonlightR, bigmelon, minfi, phantasus, recount, BeadArrayUseCases, BioPlex, GSE13015, healthyControlsPresenceChecker, easyDifferentialGeneCoexpression, geneExpressionFromGEO, seeker
Suggests Me	AUCell, COTAN, EpiDISH, EpiMix, FLAMES, GeneExpressionSignature, GenomicOZone, GeoTcgaData, MultiDataSet, PCAtools, RGSEA, RegEnrich, Rnits, TargetScore, autonomics, ctsGE, dearseq, debCAM, diffcoexp, dyebias, fgsea, methylclock, multiClust, omicsPrint, phantasusLite, quantiseqr, runibic, skewr, spatialHeatmap, zFPKM, ath1121501frmavecs, airway, antiProfilesData, muscData, parathyroidSE, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, RegParallel, AnnoProbe, BED, easybio, fdrci, maGUI, metaMA, MLML2R, NACHO, TcGSA, tinyarray
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	GEOquery_2.75.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/GEOquery
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GEOquery
Bioc Package Browser	https://code.bioconductor.org/browse/GEOquery/
Package Short Url	https://bioconductor.org/packages/GEOquery/
Package Downloads Report	Download Stats