GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Bioconductor version: 3.23 · Package version: 2.80.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/GEOquery/ |
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 2.80.0, https://bioconductor.org/packages/GEOquery.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GEOquery_2.80.0.tar.gz |
| Windows binary (x86_64) | GEOquery_2.80.0.zip |
| macOS binary (arm64) | GEOquery_2.80.0.tgz |
| macOS binary (x86_64) | GEOquery_2.80.0.tgz |
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 (17): BeadArrayUseCases, bigmelon, BioPlex, 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