GEOquery
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GEOquery.
Get data from NCBI Gene Expression Omnibus (GEO)
Bioconductor version: 3.9
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("GEOquery")):
Installation
To install this package, start R (version "3.6") 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")| Using GEOquery | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel |
| Version | 2.52.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (18 years) |
| License | GPL-2 |
| Depends | methods, Biobase |
| Imports | httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma |
| System Requirements | |
| URL | https://github.com/seandavi/GEOquery |
| Bug Reports | https://github.com/seandavi/GEOquery/issues/new |
See More
| Suggests | knitr, rmarkdown, BiocGenerics, testthat, covr |
| Linking To | |
| Enhances | |
| Depends On Me | DrugVsDisease, dyebiasexamples, GEOmetadb, GSE62944, SCAN.UPC |
| Imports Me | BeadArrayUseCases, bigmelon, ChIPXpress, coexnet, crossmeta, EGAD, GAPGOM, 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, PCAtools, PGSEA, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, RegParallel, RGSEA, Rnits, runibic, skewr, TargetScore, zFPKM |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GEOquery_2.52.0.tar.gz |
| Windows Binary | GEOquery_2.52.0.zip |
| Mac OS X 10.11 (El Capitan) | GEOquery_2.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GEOquery |
| Source Repository (Developer Access) | git clone [email protected]:packages/GEOquery |
| Bioc Package Browser | https://code.bioconductor.org/browse/GEOquery/ |
| Package Short Url | https://bioconductor.org/packages/GEOquery/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |