Get data from NCBI Gene Expression Omnibus (GEO)

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Documentation for package ‘GEOquery’ version 2.81.21

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

Accession	Accessors for GEOquery objects
Accession-method	Class 'GEOData'
Accession-method	Class 'GEODataTable'
as_SummarizedExperiment	Coerce a GEOquery ExpressionSet to a SummarizedExperiment
browseGEOAccession	Open the GEO page for a given accession
browseWebsiteRNASeqSearch	Browse GEO search website for RNA-seq datasets
clearGEOCache	Clear the GEOquery download cache
coercion	Convert a GDS data structure to a BioConductor data structure
Columns	Accessors for GEOquery objects
Columns-method	Class 'GEOData'
Columns-method	Class 'GEODataTable'
dataTable	Accessors for GEOquery objects
dataTable-method	Class 'GEOData'
dataTable-method	Class 'GEODataTable'
GDS-class	Class 'GDS'
GDS2eSet	Convert a GDS data structure to a BioConductor data structure
GDS2MA	Convert a GDS data structure to a BioConductor data structure
geoCache	GEOquery download cache
GEOData-accessors	Accessors for GEOquery objects
GEOData-class	Class 'GEOData'
GEODataTable-class	Class 'GEODataTable'
geoSingleCellManifest	Inventory the single-cell supplementary files of a GEO Series
geoSingleCellUnits	Group a single-cell manifest into loadable units
getDirListing	get a directory listing from NCBI GEO
getGEO	Get a GEO object from NCBI or file
getGEOfile	Download a file from GEO soft file to the local machine
getGEOSeriesFileListing	GSE Supplemental file listing
getGEOSingleCell	Download and read the single-cell data of a GEO Series
getGEOSuppFiles	Get Supplemental Files from GEO
getGEOSuppFileURL	Get GEO supplemental file URL for a given GEO accession
getGSEDataTables	Get GSE data tables from GEO into R data structures.
getRNASeqData	Get GEO RNA-seq quantifications as a SummarizedExperiment object
getRNASeqQuantGenomeInfo	Extract genome build and species for GEO RNA-seq quantification
GPL	Class 'GPL'
GPL-class	Class 'GPL'
GPL-method	Class 'GPL'
GPLList	Accessors for GEOquery objects
GPLList-method	Class 'GSE'
GSE-class	Class 'GSE'
GSM-class	Class 'GSM'
GSMList	Accessors for GEOquery objects
GSMList-method	Class 'GSE'
hasRNASeqQuantifications	Does a GEO accession have RNA-seq quantifications?
Meta	Accessors for GEOquery objects
Meta-method	Class 'GEOData'
Meta-method	Class 'GEODataTable'
Meta-method	Class 'GSE'
parseGDS	Parse GEO text
parseGEO	Parse GEO text
parseGPL	Parse GEO text
parseGSE	Parse GEO text
parseGSM	Parse GEO text
readGEOSingleCell	Read a single-cell file (or 10x triplet) into a SingleCellExperiment
searchFieldsGEO	Provide a list of possible search fields for GEO search
searchGEO	Search GEO database
show-method	Class 'GEOData'
show-method	Class 'GEODataTable'
Table	Accessors for GEOquery objects
Table-method	Class 'GEOData'
Table-method	Class 'GEODataTable'
urlForAccession	The URL for a GEO accession