GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)
Version 2.42.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorSean Davis <sdavis2@mail.nih.gov>
Bioconductor views DataImport Microarray OneChannel SAGE TwoChannel
Date of publicationNone
MaintainerSean Davis <sdavis2@mail.nih.gov>
LicenseGPL-2
Version2.42.0
URL https://github.com/seandavi/GEOquery
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GEOquery")

Man pages

dataTable: Generic functions for GEOquery
GDS2MA: Convert a GDS data structure to a BioConductor data structure
GDS-class: Class "GDS"
GEOData-class: Class "GEOData"
GEODataTable-class: Class "GEODataTable"
getGEO: Get a GEO object from NCBI or file
getGEOfile: Download a file from GEO soft file to the local machine
getGEOSuppFiles: Get Supplemental Files from GEO
getGSEDataTables: Get GSE data tables from GEO into R data structures.
GPL-class: Class "GPL"
GSE-class: Class "GSE"
GSM-class: Class "GSM"
gunzip: Gunzip a file
parseGEO: Parse GEO text

Functions

Accession Man page
Accession,GEOData-method Man page
Accession,GEODataTable-method Man page
Columns Man page
Columns,GEOData-method Man page
Columns,GEODataTable-method Man page
GDS-class Man page
GDS2MA Man page
GDS2eSet Man page
GEOData-class Man page
GEODataTable-class Man page
GPL-class Man page
GPLList Man page
GPLList,GSE-method Man page
GSE-class Man page
GSM-class Man page
GSMList Man page
GSMList,GSE-method Man page
Meta Man page
Meta,GEOData-method Man page
Meta,GEODataTable-method Man page
Meta,GSE-method Man page
Table Man page
Table,GEOData-method Man page
Table,GEODataTable-method Man page
chopColumns Source code
dataTable Man page
dataTable,GEOData-method Man page
dataTable,GEODataTable-method Man page
fastTabRead Source code
fileOpen Source code
filegrep Source code
findFirstEntity Source code
getAndParseGSEMatrices Source code
getDirListing Source code
getGEO Man page Source code
getGEORaw Source code
getGEOSuppFiles Man page Source code
getGEOfile Man page Source code
getGSEDataTables Man page Source code
gunzip Man page Source code
onLoad Source code
parseGDS Man page Source code
parseGDSSubsets Source code
parseGEO Man page Source code
parseGPL Man page Source code
parseGPLWithLimits Source code
parseGSE Man page Source code
parseGSEMatrix Source code
parseGSM Man page Source code
parseGSMWithLimits Source code
parseGeoColumns Source code
parseGeoMeta Source code
printHead Source code
show,GEOData-method Man page
show,GEODataTable-method Man page
splitOnFirst Source code
txtGrab Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GDS2MA.R
R/classes.R
R/fileOpen.R
R/getGEO.R
R/getGEOSuppFiles.R
R/getGEOfile.R
R/getGSEDataTables.R
R/parseGEO.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/GEOquery.R
inst/doc/GEOquery.Rmd
inst/doc/GEOquery.html
inst/extdata
inst/extdata/GDS507.soft.gz
inst/extdata/GPL97.annot.gz
inst/extdata/GSE781_family.soft.gz
inst/extdata/GSM11805.txt.gz
inst/unitTests
inst/unitTests/test_CaseMismatchedIDsGSE.R
inst/unitTests/test_EmptyGSE.R
inst/unitTests/test_GDSConversions.R
inst/unitTests/test_GenericGDS.R
inst/unitTests/test_GenericGPL.R
inst/unitTests/test_GenericGSM.R
inst/unitTests/test_QuotedGPL.R
inst/unitTests/test_SOFTFormatGSE.R
inst/unitTests/test_ShortGPL.R
inst/unitTests/test_ShortGSE.R
inst/unitTests/test_SingleSampleGSE.R
inst/unitTests/test_SuppFileSupport.R
inst/unitTests/test_getGPLFALSE.R
man
man/GDS-class.Rd
man/GDS2MA.Rd
man/GEOData-class.Rd
man/GEODataTable-class.Rd
man/GPL-class.Rd
man/GSE-class.Rd
man/GSM-class.Rd
man/dataTable.Rd
man/getGEO.Rd
man/getGEOSuppFiles.Rd
man/getGEOfile.Rd
man/getGSEDataTables.Rd
man/gunzip.Rd
man/parseGEO.Rd
tests
tests/runTests.R
vignettes
vignettes/GEOquery.Rmd
GEOquery documentation built on May 20, 2017, 10:25 p.m.