Package: GEOquery 2.81.28

Sean Davis

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

The NCBI Gene Expression Omnibus (GEO) is a public repository of high-throughput functional genomics data, including microarray, RNA-seq, and single-cell experiments. GEOquery is the bridge between GEO and Bioconductor: it downloads and parses GEO Series (GSE), Sample (GSM), Platform (GPL), and DataSet (GDS) records. By default it parses GEO Series Matrix files into Bioconductor 'ExpressionSet' objects; it can also parse the full SOFT format into GEOquery's own S4 classes, retrieve NCBI-computed RNA-seq quantifications, download supplementary files, and search GEO.

Authors:Sean Davis [aut, cre]

GEOquery_2.81.28.tar.gz
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GEOquery_2.81.28.tgz(r-4.6-any)GEOquery_2.81.28.tgz(r-4.5-any)
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GEOquery_2.81.28.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.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-2.81.21(bioc 3.24)GEOquery-2.80.0(bioc 3.23)

geneexpressiontranscriptomicsmicroarrayrnaseqsequencingsinglecelldataimportthirdpartyclientonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geou24ca289073quarto

15.93 score 115 stars 52 packages 6.3k scripts 19k downloads 328 mentions 33 exports 74 dependencies

Last updated from:504d4d30a8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR234
linux-devel-x86_64NOTE375
source / vignettesOK337
linux-release-x86_64NOTE365
macos-release-arm64NOTE216
macos-oldrel-arm64NOTE193
windows-develNOTE295
windows-releaseNOTE302
windows-oldrelNOTE281
wasm-releaseOK186

Exports:Accessionas_SummarizedExperimentbrowseGEOAccessionbrowseWebsiteRNASeqSearchclearGEOCacheColumnsdataTableGDS2eSetGDS2MAgeoCachegeoSingleCellManifestgeoSingleCellUnitsgetGEOgetGEOfilegetGEOSeriesFileListinggetGEOSingleCellgetGEOSuppFilesgetGEOSuppFileURLgetGSEDataTablesgetRNASeqDatagetRNASeqQuantGenomeInfoGPLGPLListGSMListhasRNASeqQuantificationsMetaparseGEOreadGEOSingleCellsearchFieldsGEOsearchGEOshowTableurlForAccession

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicliprcpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrfastmapfilelockgenericsGenomicRangesgluehmshttrhttr2IRangesjsonlitelatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6readrrentrezrlangRSQLitervestS4ArraysS4VectorsselectrSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2XVector

Finding and downloading data
Finding studies from R | Controlling what getGEO() fetches | Supplementary files | Caching and reproducibility | Private and embargoed records | Where to go next
Rendered fromfinding-and-downloading-data.qmdusingquarto::html

Last update: 2026-07-18
Started: 2026-07-18

From GEO to downstream analysis
Know your object | Microarray: limma | RNA-seq counts: DESeq2 / edgeR / limma-voom | Single cell: the OSCA stack | Converting and annotating | Reproducibility | Where to go next
Rendered fromdownstream-analysis.qmdusingquarto::html

Last update: 2026-07-18
Started: 2026-07-18

Getting started with GEOquery
Install | Your first record | The other entity types | Peeking at supplementary files | Where to go next | Getting help
Rendered fromGEOquery.qmdusingquarto::html

Last update: 2026-07-18
Started: 2025-08-16

RNA-seq quantifications from GEO
NCBI-computed quantifications vs. submitter files | Checking availability and loading | Why raw counts (and what to do with them) | When you need the submitter's files instead | Where to go next
Rendered fromrnaseq.qmdusingquarto::html

Last update: 2026-07-18
Started: 2026-07-18

Single-cell data from GEO
Why single-cell data is different | The file formats you will meet | Step 1 — inspect: the manifest | Step 2 — decide: loadable units | Step 3 — load | Sample metadata travels with the cells | Full control | The reader dependencies | Working with Seurat | Downstream: the single-cell ecosystem | What is intentionally out of scope | Where to go next
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Last update: 2026-07-18
Started: 2025-09-03

Understanding GEO data formats
The four GEO entity types | Two file formats, two code paths | SOFT — the complete, verbose record | Series Matrix — the fast, analysis-ready path | Why getGEO() returns different classes | ExpressionSet vs. SummarizedExperiment | Supplementary files: where everything else lives | Where to go next
Rendered fromgeo-data-formats.qmdusingquarto::html

Last update: 2026-07-18
Started: 2026-07-18

Readme and manuals

Help Manual

Help pageTopics
Coerce a GEOquery ExpressionSet to a SummarizedExperimentas_SummarizedExperiment
Open the GEO page for a given accessionbrowseGEOAccession
Browse GEO search website for RNA-seq datasetsbrowseWebsiteRNASeqSearch
Clear the GEOquery download cacheclearGEOCache
Convert a GDS data structure to a BioConductor data structurecoercion GDS2eSet GDS2MA
Class 'GDS'GDS-class
GEOquery download cachegeoCache
Accessors for GEOquery objectsAccession 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
Inventory the single-cell supplementary files of a GEO Series or SamplegeoSingleCellManifest
Group a single-cell manifest into loadable unitsgeoSingleCellUnits
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
Download and read the single-cell data of a GEO Series or SamplegetGEOSingleCell
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
Read a single-cell file (or 10x triplet) into a SingleCellExperimentreadGEOSingleCell
Provide a list of possible search fields for GEO searchsearchFieldsGEO
Search GEO databasesearchGEO
The URL for a GEO accessionurlForAccession