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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 (3.20)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") 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
NEWS Text
LICENSE Text

Details

biocViews DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel
Version 2.73.0
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
URL https://github.com/seandavi/GEOquery http://seandavi.github.io/GEOquery
Bug Reports https://github.com/seandavi/GEOquery/issues/new
See More
Suggests knitr, rmarkdown, BiocGenerics, testthat, covr, markdown
Linking To
Enhances
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
Build Report Build Report

Package Archives

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

Source Package GEOquery_2.73.0.tar.gz
Windows Binary GEOquery_2.73.0.zip
macOS Binary (x86_64) GEOquery_2.73.0.tgz
macOS Binary (arm64) GEOquery_2.73.0.tgz
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