Package: GEOquery 2.80.0

Sean Davis

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

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.

Authors:Sean Davis [aut, cre]

GEOquery_2.80.0.tar.gz
GEOquery_2.80.0.zip(r-4.7-any)GEOquery_2.80.0.zip(r-4.6-any)GEOquery_2.80.0.zip(r-4.5-any)
GEOquery_2.80.0.tgz(r-4.6-any)GEOquery_2.80.0.tgz(r-4.5-any)
GEOquery_2.80.0.tar.gz(r-4.7-any)GEOquery_2.80.0.tar.gz(r-4.6-any)
GEOquery_2.80.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GEOquery/json (API)

# Install 'GEOquery' in R:
install.packages('GEOquery', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/seandavi/geoquery/issues

Pkgdown/docs site:https://seandavi.github.io

On BioConductor:GEOquery-2.81.28(bioc 3.24)GEOquery-2.80.0(bioc 3.23)

microarraydataimportonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geou24ca289073quarto

15.10 score 117 stars 54 packages 6.4k scripts 27k downloads 328 mentions 26 exports 65 dependencies

Last updated from:8b846af9fe (on RELEASE_3_23). Checks:8 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR190
linux-develERROR362
source / vignettesOK303
linux-releaseERROR367
macos-releaseERROR318
macos-oldrelERROR233
windows-develERROR349
windows-releaseERROR371
windows-oldrelERROR359
wasm-releaseOK155

Exports:AccessionbrowseGEOAccessionbrowseWebsiteRNASeqSearchColumnsdataTableGDS2eSetGDS2MAgetGEOgetGEOfilegetGEOSeriesFileListinggetGEOSuppFilesgetGEOSuppFileURLgetGSEDataTablesgetRNASeqDatagetRNASeqQuantGenomeInfoGPLGPLListGSMListhasRNASeqQuantificationsMetaparseGEOsearchFieldsGEOsearchGEOshowTableurlForAccession

Dependencies:abindaskpassBiobaseBiocGenericsbitbit64clicliprcpp11crayoncurldata.tableDelayedArraydplyrgenericsGenomicRangesgluehmshttrhttr2IRangesjsonlitelatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6readrrentrezrlangrvestS4ArraysS4VectorsselectrSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2XVector

Handling single-cell RNA-seq data in GEOquery
Single cell searching | Mtx files | Multiple h5ad files | Single h5ad file | SAMPLES | mtx file | Tar of mtx files from Series record | Mix of types in a single GSE | 10x h5 file | 10x matrix mtx files
Rendered fromsingle-cell.qmdusingquarto::html

Last update: 2025-09-03
Started: 2025-09-03

Using GEOquery (Quarto)
Introduction to GEO and GEOquery | Why GEOquery? | GEO Data Organization | Getting Started with GEOquery | Downloading a GEO Series | Historical Context: SOFT Format vs GSEMatrix Files | Searching GEO Programmatically | RNA-seq Quantifications: NCBI's Solution to Reanalysis Challenges | The Challenge of RNA-seq Reanalysis | NCBI's RNA-seq Quantification Pipeline | Understanding Supplementary Files in GEO | Navigating Between R and the GEO Web Interface | Working with GDS Datasets | Advanced Features | Getting GSE Data Tables | Working with GPL Platforms | Reporting Bugs and Contributing | Citing GEOquery | Session Information
Rendered fromGEOquery.qmdusingquarto::html

Last update: 2025-09-03
Started: 2025-08-16

Readme and manuals

Help Manual

Help pageTopics
Open the GEO page for a given accessionbrowseGEOAccession
Browse GEO search website for RNA-seq datasetsbrowseWebsiteRNASeqSearch
Convert a GDS data structure to a BioConductor data structurecoercion GDS2eSet GDS2MA
Class 'GDS'GDS-class
Generic functions for GEOqueryAccession Columns dataTable GEOData-accessors GPLList GSMList Meta Table
Class 'GEOData'Accession,GEOData-method Columns,GEOData-method dataTable,GEOData-method GEOData-class Meta,GEOData-method show,GEOData-method Table,GEOData-method
Class 'GEODataTable'Accession,GEODataTable-method Columns,GEODataTable-method dataTable,GEODataTable-method GEODataTable-class Meta,GEODataTable-method show,GEODataTable-method Table,GEODataTable-method
get a directory listing from NCBI GEOgetDirListing
Get a GEO object from NCBI or filegetGEO
Download a file from GEO soft file to the local machinegetGEOfile
GSE Supplemental file listinggetGEOSeriesFileListing
Get Supplemental Files from GEOgetGEOSuppFiles
Get GEO supplemental file URL for a given GEO accessiongetGEOSuppFileURL
Get GSE data tables from GEO into R data structures.getGSEDataTables
Get GEO RNA-seq quantifications as a SummarizedExperiment objectgetRNASeqData
Extract genome build and species for GEO RNA-seq quantificationgetRNASeqQuantGenomeInfo
Class 'GPL'GPL GPL,GDS-method GPL-class
Class 'GSE'GPLList,GSE-method GSE-class GSMList,GSE-method Meta,GSE-method
Class 'GSM'GSM-class
Does a GEO accession have RNA-seq quantifications?hasRNASeqQuantifications
Parse GEO textparseGDS parseGEO parseGPL parseGSE parseGSM
Provide a list of possible search fields for GEO searchsearchFieldsGEO
Search GEO databasesearchGEO
The URL for a GEO accessionurlForAccession