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A compilation of metadata from NCBI GEO

Bioconductor version: Release (3.18)

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .

Author: Jack Zhu and Sean Davis

Maintainer: Jack Zhu <zhujack at mail.nih.gov>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

GEOmetadb HTML R Script
Reference Manual PDF


biocViews Infrastructure, Software
Version 1.64.0
In Bioconductor since BioC 2.2 (R-2.7) (16 years)
License Artistic-2.0
Depends GEOquery, RSQLite
System Requirements
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Suggests knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud
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Depends On Me
Imports Me MetaIntegrator
Suggests Me antiProfilesData
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Follow Installation instructions to use this package in your R session.

Source Package GEOmetadb_1.64.0.tar.gz
Windows Binary GEOmetadb_1.64.0.zip
macOS Binary (x86_64) GEOmetadb_1.64.0.tgz
macOS Binary (arm64) GEOmetadb_1.64.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GEOmetadb
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GEOmetadb
Bioc Package Browser https://code.bioconductor.org/browse/GEOmetadb/
Package Short Url https://bioconductor.org/packages/GEOmetadb/
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