Get data from NCBI Gene Expression Omnibus (GEO)


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Documentation for package ‘GEOquery’ version 2.74.0

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Accession Generic functions for GEOquery
Accession-method Class 'GEOData'
Accession-method Class 'GEODataTable'
browseGEOAccession Open the GEO page for a given accession
browseWebsiteRNASeqSearch Browse GEO search website for RNA-seq datasets
coercion Convert a GDS data structure to a BioConductor data structure
Columns Generic functions for GEOquery
Columns-method Class 'GEOData'
Columns-method Class 'GEODataTable'
dataTable Generic functions for GEOquery
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
GEOData-accessors Generic functions for GEOquery
GEOData-class Class 'GEOData'
GEODataTable-class Class 'GEODataTable'
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
getGEOSuppFiles Get Supplemental Files from GEO
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 Generic functions for GEOquery
GPLList-method Class 'GSE'
GSE-class Class 'GSE'
GSM-class Class 'GSM'
GSMList Generic functions for GEOquery
GSMList-method Class 'GSE'
hasRNASeqQuantifications Does a GEO accession have RNA-seq quantifications?
Meta Generic functions for GEOquery
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
searchFieldsGEO Provide a list of possible search fields for GEO search
searchGEO Search GEO database
show-method Class 'GEOData'
show-method Class 'GEODataTable'
Table Generic functions for GEOquery
Table-method Class 'GEOData'
Table-method Class 'GEODataTable'
urlForAccession The URL for a GEO accession