GEOquery

Get data from NCBI Gene Expression Omnibus (GEO)

Bioconductor version: 3.23 · Package version: 2.80.0

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.

Installation

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

BiocManager::install("GEOquery")

Details

Maintainer	Sean Davis <seandavi@gmail.com>
Author	Sean Davis [aut, cre] (ORCID: <https://orcid.org/0000-0002-8991-6458>)
License	MIT + file LICENSE
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
Downloads rank	14239
Source branch	RELEASE_3_23
biocViews	DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel

Documentation

Download

Source package

Dependencies

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

Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown, quarto, DropletUtils, SingleCellExperiment

Reverse dependencies

Depends On Me (6): DrugVsDisease, dyebiasexamples, GSE103322, GSE13015, GSE62944, SCAN.UPC

Imports Me (18): BeadArrayUseCases, bigmelon, BioPlex, BioUtils, ChIPXpress, COTAN, DExMA, EGAD, geneExpressionFromGEO, GEOexplorer, GSE13015, healthyControlsPresenceChecker, minfi, Moonlight2R, MoonlightR, phantasus, RCPA, recount

Suggests Me (51): airway, AnnoProbe, antiProfilesData, ath1121501frmavecs, AUCell, autonomics, BED, CimpleG, ctsGE, dearseq, diffcoexp, dyebias, easybio, EpiDISH, EpiMix, epiSeeker, fdrci, fgsea, FLAMES, GeneExpressionSignature, GenomicOZone, GeoTcgaData, maGUI, metaMA, methylclock, MLML2R, multiClust, MultiDataSet, muscData, NACHO, omicsPrint, PCAtools, phantasusLite, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, quantiseqr, RegEnrich, RegParallel, RFGeneRank, RGSEA, Rnits, scregclust, skewr, spatialHeatmap, TargetScore, TcGSA, tinyarray, zFPKM