- Home
- Bioconductor 3.5
- Software Packages
- GEOquery
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GEOquery")
In most cases, you don't need to download the package archive at all.
GEOquery
|
|
|
|
|
Get data from NCBI Gene Expression Omnibus (GEO)
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GEOquery")
Documentation
| HTML | R Script | Using GEOquery |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel |
| Version | 2.42.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (11.5 years) |
| License | GPL-2 |
| Depends | methods, Biobase |
| Imports | XML, RCurl, httr |
| LinkingTo | |
| Suggests | limma, knitr, rmarkdown, RUnit, BiocGenerics |
| 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 | AnnotationHubData, BeadArrayUseCases, bigmelon, ChIPXpress, crossmeta, EGAD, minfi, MoonlightR, recount, SRAdb |
| Suggests Me | airway, antiProfilesData, ctsGE, dyebias, ELBOW, GeneExpressionSignature, multiClust, MultiDataSet, parathyroidSE, pathprint, PGSEA, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, RGSEA, RnBeads, Rnits, skewr, TargetScore |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GEOquery_2.42.0.tar.gz |
| Windows Binary | GEOquery_2.42.0.zip |
| Mac OS X 10.11 (El Capitan) | GEOquery_2.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GEOquery |
| Package Short Url | http://bioconductor.org/packages/GEOquery/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
