GEOquery

DOI: 10.18129/B9.bioc.GEOquery    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see GEOquery.

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: 3.14

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 <sdavis2 at mail.nih.gov>

Maintainer: Sean Davis <sdavis2 at mail.nih.gov>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	Using GEOquery
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel
Version	2.62.2
In Bioconductor since	BioC 1.8 (R-2.3) (16 years)
License	GPL-2
Depends	methods, Biobase
Imports	httr, readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, R.utils, limma
LinkingTo
Suggests	knitr, rmarkdown, BiocGenerics, testthat, covr, markdown
SystemRequirements
Enhances
URL	https://github.com/seandavi/GEOquery
BugReports	https://github.com/seandavi/GEOquery/issues/new
Depends On Me	DrugVsDisease, dyebiasexamples, GEOmetadb, GSE103322, GSE13015, GSE62944, SCAN.UPC
Imports Me	BeadArrayUseCases, bigmelon, BioPlex, ChIPXpress, coexnet, conclus, crossmeta, DExMA, EGAD, GAPGOM, GEOexplorer, GSE13015, MACPET, minfi, MoonlightR, phantasus, recount, SRAdb
Suggests Me	airway, antiProfilesData, AUCell, autonomics, ctsGE, dearseq, debCAM, diffcoexp, dyebias, EpiDISH, fgsea, GCSscore, GeneExpressionSignature, GenomicOZone, methylclock, multiClust, MultiDataSet, muscData, omicsPrint, parathyroidSE, PCAtools, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, quantiseqr, RegEnrich, RegParallel, RGSEA, Rnits, runibic, skewr, spatialHeatmap, TargetScore, zFPKM
Links To Me
Build Report

Package Archives

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

Source Package	GEOquery_2.62.2.tar.gz
Windows Binary	GEOquery_2.62.2.zip
macOS 10.13 (High Sierra)	GEOquery_2.62.2.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