GEOquery

This is the development version of GEOquery; for the stable release version, see GEOquery.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: Development (3.24)

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.

Author: Sean Davis [aut, cre] ORCID: 0000-0002-8991-6458

Maintainer: Sean Davis <seandavi at gmail.com>

Citation (from within R, enter citation("GEOquery")):

Sean Davis. GEOquery: Get data from NCBI Gene Expression Omnibus (GEO). doi:10.18129/B9.bioc.GEOquery, R package version 2.81.28, https://bioconductor.org/packages/GEOquery.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("GEOquery")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GEOquery")

downstream-analysis.html	HTML
finding-and-downloading-data.html	HTML
geo-data-formats.html	HTML
GEOquery.html	HTML
rnaseq.html	HTML
single-cell.html	HTML
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GeneExpression, Microarray, OneChannel, RNASeq, SAGE, Sequencing, SingleCell, Software, ThirdPartyClient, Transcriptomics, TwoChannel
Version	2.81.28
In Bioconductor since	BioC 1.8 (R-2.3) (20.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), methods, Biobase
Imports	readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2, rlang, BiocFileCache
System Requirements
URL	https://github.com/seandavi/GEOquery http://seandavi.github.io/GEOquery http://seandavi.github.io/GEOquery/
Bug Reports	https://github.com/seandavi/GEOquery/issues/new

Suggests	knitr, rmarkdown, BiocGenerics, testthat, covr, markdown, quarto, SingleCellExperiment, TENxIO, anndataR, BiocIO, Seurat
Linking To
Enhances
Depends On Me	DrugVsDisease, dyebiasexamples, GSE103322, GSE13015, GSE62944, SCAN.UPC
Imports Me	BeadArrayUseCases, bigmelon, BioPlex, ChIPXpress, COTAN, DExMA, EGAD, geneExpressionFromGEO, GExPipe, GSE13015, healthyControlsPresenceChecker, minfi, Moonlight2R, MoonlightR, phantasus, RCPA, recount
Suggests Me	airway, AnnoProbe, antiProfilesData, ath1121501frmavecs, AUCell, autonomics, BED, BenchHub, CimpleG, ctsGE, dearseq, diffcoexp, dyebias, easybio, EpiDISH, EpiMix, epiSeeker, fdrci, fgsea, FLAMES, GeneExpressionSignature, GenomicOZone, GeoTcgaData, maGUI, metaMA, MLML2R, multiClust, MultiDataSet, MultiOmicsBridge, muscData, NACHO, omicsPrint, PCAtools, phantasusLite, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, quantiseqr, RegEnrich, RegParallel, RFGeneRank, RGSEA, rnaSentry, Rnits, scregclust, skewr, spatialHeatmap, TargetScore, TcGSA, tinyarray, zFPKM
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GEOquery_2.81.28.tar.gz
Windows Binary (x86_64)	GEOquery_2.81.28.zip (64-bit only)
macOS Binary (big-sur-x86_64)	GEOquery_2.81.28.tgz
macOS Binary (sonoma-arm64)	GEOquery_2.81.28.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GEOquery
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GEOquery
Package Short Url	https://bioconductor.org/packages/GEOquery/
Package Downloads Report	Download Stats