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

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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@mail.nih.gov>
Date of publication
None
Maintainer
Sean Davis <sdavis2@mail.nih.gov>
License
GPL-2
Version
2.40.0
URLs

View on Bioconductor

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

Files in this package

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