Package: GEOquery 2.75.0

Sean Davis

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

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.

Authors:Sean Davis [aut, cre]

GEOquery_2.75.0.tar.gz
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GEOquery.pdf |GEOquery.html✨
GEOquery/json (API)
NEWS

# 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 site:https://seandavi.github.io

On BioConductor:GEOquery-2.75.0(bioc 3.21)GEOquery-2.74.0(bioc 3.20)

microarray dataimport onechannel twochannel sage bioconductor bioinformatics data-science genomics ncbi-geo

14.53 score 90 stars 53 packages 4.1k scripts 15k downloads 328 mentions 24 exports 69 dependencies

Last updated 4 months agofrom:2a416df48b. Checks:1 OK, 6 NOTE, 1 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 28 2025
R-4.5-win	NOTE	Jan 28 2025
R-4.5-mac	ERROR	Jan 28 2025
R-4.5-linux	NOTE	Jan 28 2025
R-4.4-win	NOTE	Jan 28 2025
R-4.4-mac	NOTE	Jan 28 2025
R-4.3-win	NOTE	Jan 28 2025
R-4.3-mac	NOTE	Jan 28 2025

Exports:Accession browseGEOAccession browseWebsiteRNASeqSearch Columns dataTable GDS2eSet GDS2MA getGEO getGEOfile getGEOSuppFiles getGSEDataTables getRNASeqData getRNASeqQuantGenomeInfo GPL GPLList GSMList hasRNASeqQuantifications Meta parseGEO searchFieldsGEO searchGEO show Table urlForAccession

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

Using the GEOquery Package

Sean Davis

Rendered fromGEOquery.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2022-05-11
Started: 2014-09-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Open the GEO page for a given accession	browseGEOAccession
Browse GEO search website for RNA-seq datasets	browseWebsiteRNASeqSearch
Convert a GDS data structure to a BioConductor data structure	coercion GDS2eSet GDS2MA
Class 'GDS'	GDS-class
Generic functions for GEOquery	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
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
Get Supplemental Files from GEO	getGEOSuppFiles
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
Provide a list of possible search fields for GEO search	searchFieldsGEO
Search GEO database	searchGEO
The URL for a GEO accession	urlForAccession