GEOquery

DOI: 10.18129/B9.bioc.GEOquery    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GEOquery.

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: 3.8

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>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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 2.50.5
In Bioconductor since BioC 1.8 (R-2.3) (13 years)
License GPL-2
Depends methods, Biobase
Imports httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma
LinkingTo
Suggests knitr, rmarkdown, BiocGenerics, testthat, covr
SystemRequirements
Enhances
URL https://github.com/seandavi/GEOquery
BugReports https://github.com/seandavi/GEOquery/issues/new
Depends On Me DrugVsDisease, dyebiasexamples, GEOmetadb, GSE62944, SCAN.UPC
Imports Me BeadArrayUseCases, bigmelon, ChIPXpress, coexnet, crossmeta, EGAD, GSEABenchmarkeR, MACPET, minfi, MoonlightR, phantasus, recount, SRAdb
Suggests Me airway, antiProfilesData, AUCell, CAMTHC, ctsGE, diffcoexp, dyebias, ELBOW, EpiDISH, fgsea, GeneExpressionSignature, multiClust, MultiDataSet, omicsPrint, parathyroidSE, pathprint, PGSEA, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, RegParallel, RGSEA, Rnits, runibic, skewr, TargetScore, zFPKM
Links To Me
Build Report  

Package Archives

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

Source Package GEOquery_2.50.5.tar.gz
Windows Binary GEOquery_2.50.5.zip
Mac OS X 10.11 (El Capitan) GEOquery_2.50.5.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 http://bioconductor.org/packages/GEOquery/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: