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Bioconductor - GEOquery

GEOquery

This is the released version of GEOquery; for the devel version, see GEOquery.

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: Release (3.21)

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.

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

Maintainer: Sean Davis <seandavi at gmail.com>

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

To install this package, start R (version "4.5") and enter:


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

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")

Details biocViews DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel Version 2.76.0 In Bioconductor since BioC 1.8 (R-2.3) (19 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 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 See More Suggests knitr, rmarkdown, BiocGenerics, testthat, covr, markdown Linking To Enhances Depends On Me DrugVsDisease, SCAN.UPC, dyebiasexamples, GSE103322, GSE13015, GSE62944 Imports Me bigmelon, ChIPXpress, DExMA, EGAD, GEOexplorer, minfi, Moonlight2R, MoonlightR, phantasus, recount, BeadArrayUseCases, BioPlex, GSE13015, healthyControlsPresenceChecker, geneExpressionFromGEO, RCPA Suggests Me AUCell, autonomics, COTAN, ctsGE, dearseq, debCAM, diffcoexp, dyebias, EpiDISH, EpiMix, fgsea, FLAMES, GeneExpressionSignature, GenomicOZone, GeoTcgaData, methylclock, multiClust, MultiDataSet, omicsPrint, PCAtools, phantasusLite, quantiseqr, RegEnrich, RGSEA, Rnits, runibic, skewr, spatialHeatmap, TargetScore, zFPKM, ath1121501frmavecs, airway, antiProfilesData, muscData, parathyroidSE, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, RegParallel, AnnoProbe, BED, easybio, fdrci, maGUI, metaMA, MLML2R, NACHO, TcGSA, tinyarray Links To Me Build Report Build Report Package Archives

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

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