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To install this package, start R and enter:
source("http://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: 3.0
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:
source("http://bioconductor.org/biocLite.R")
biocLite("GEOquery")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GEOquery")
| R Script | GEOquery.pdf | |
| HTML | R Script | Using GEOquery |
| Reference Manual |
Details
| biocViews | DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel |
| Version | 2.32.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) |
| License | GPL-2 |
| Depends | methods, Biobase |
| Imports | XML, RCurl |
| LinkingTo | |
| Suggests | limma, knitr, rmarkdown |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/seandavi/GEOquery |
| Depends On Me | DrugVsDisease, dyebiasexamples, GEOmetadb, SCAN.UPC |
| Imports Me | BeadArrayUseCases, ChIPXpress, SRAdb |
| Suggests Me | airway, antiProfilesData, dyebias, ELBOW, GeneExpressionSignature, parathyroid, parathyroidSE, PGSEA, RGSEA, Rnits, TargetScore |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GEOquery_2.32.0.tar.gz |
| Windows Binary | GEOquery_2.32.0.zip |
| Mac OS X 10.6 (Snow Leopard) | GEOquery_2.32.0.tgz |
| Mac OS X 10.9 (Mavericks) | GEOquery_2.32.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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