Package index • GEOquery

All functions

GDS-class: Class 'GDS'

GEOData-accessors dataTable Accession Columns GPLList GSMList Meta Table: Generic functions for GEOquery

GEOData-class Accession,GEOData-method Columns,GEOData-method Meta,GEOData-method Table,GEOData-method dataTable,GEOData-method show,GEOData-method: Class 'GEOData'

GEODataTable-class Accession,GEODataTable-method Columns,GEODataTable-method Meta,GEODataTable-method Table,GEODataTable-method dataTable,GEODataTable-method show,GEODataTable-method: Class 'GEODataTable'

GPL-class GPL GPL,GDS-method: Class 'GPL'

GSE-class GPLList,GSE-method GSMList,GSE-method Meta,GSE-method: Class 'GSE'

GSM-class: Class 'GSM'

browseGEOAccession(): Open the GEO page for a given accession

browseWebsiteRNASeqSearch(): Browse GEO search website for RNA-seq datasets

coercion GDS2MA GDS2eSet: Convert a GDS data structure to a BioConductor data structure

getDirListing(): get a directory listing from NCBI GEO

getGEO(): Get a GEO object from NCBI or file

getGEOSuppFiles(): Get Supplemental Files from GEO

getGEOfile(): Download a file from GEO soft file to the local machine

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

hasRNASeqQuantifications(): Does a GEO accession have RNA-seq quantifications?

parseGEO(): Parse GEO text

searchFieldsGEO(): Provide a list of possible search fields for GEO search

searchGEO(): Search GEO database

urlForAccession(): The URL for a GEO accession