Package: GEOquery 2.81.21

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_2.81.21.tar.gz
GEOquery_2.81.21.zip(r-4.7)GEOquery_2.81.21.zip(r-4.6)GEOquery_2.81.21.zip(r-4.5)
GEOquery_2.81.21.tgz(r-4.6-any)GEOquery_2.81.0.tgz(r-4.5-any)
GEOquery_2.81.21.tar.gz(r-4.7-any)GEOquery_2.81.21.tar.gz(r-4.6-any)
GEOquery_2.81.21.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-2.81.0(bioc 3.24)GEOquery-2.80.0(bioc 3.23)

geneexpression transcriptomics microarray rnaseq sequencing singlecell dataimport thirdpartyclient onechannel twochannel sage bioconductor bioinformatics data-science genomics ncbi-geo u24ca289073 quarto

15.02 score 112 stars 52 packages 5.8k scripts 18k downloads 328 mentions 33 exports 75 dependencies

Last updated from:0d487a73b3. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	189
linux-devel-x86_64	NOTE	335
source / vignettes	OK	283
linux-release-x86_64	NOTE	334
macos-release-arm64	NOTE	209
macos-oldrel-arm64	NOTE	184
windows-devel	NOTE	268
windows-release	NOTE	264
windows-oldrel	NOTE	294
wasm-release	OK	158

Exports:Accession as_SummarizedExperiment browseGEOAccession browseWebsiteRNASeqSearch clearGEOCache Columns dataTable GDS2eSet GDS2MA geoCache geoSingleCellManifest geoSingleCellUnits getGEO getGEOfile getGEOSeriesFileListing getGEOSingleCell getGEOSuppFiles getGEOSuppFileURL getGSEDataTables getRNASeqData getRNASeqQuantGenomeInfo GPL GPLList GSMList hasRNASeqQuantifications Meta parseGEO readGEOSingleCell searchFieldsGEO searchGEO show Table urlForAccession

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli clipr cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr fastmap filelock generics GenomicRanges glue hms httr httr2 IRanges jsonlite lattice lifecycle limma magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs readr rentrez rlang RSQLite rvest S4Arrays S4Vectors selectr Seqinfo SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr XML xml2 XVector

Getting started with GEOquery

Install | Quick start | In-depth articles | Getting help

Rendered fromGEOquery.qmdusingquarto::html

Last update: 2026-06-14
Started: 2025-08-16

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

Package: GEOquery 2.81.21

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

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