Package: GEOmetadb 1.75.0

Jack Zhu

GEOmetadb: A compilation of metadata from NCBI GEO

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

Authors:Jack Zhu and Sean Davis

GEOmetadb_1.75.0.tar.gz
GEOmetadb_1.75.0.zip(r-4.7)GEOmetadb_1.75.0.zip(r-4.6)GEOmetadb_1.75.0.zip(r-4.5)
GEOmetadb_1.75.0.tgz(r-4.6-any)GEOmetadb_1.75.0.tgz(r-4.5-any)
GEOmetadb_1.75.0.tar.gz(r-4.7-any)GEOmetadb_1.75.0.tar.gz(r-4.6-any)
GEOmetadb_1.75.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GEOmetadb/json (API)

# Install 'GEOmetadb' in R:
install.packages('GEOmetadb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:GEOmetadb-1.75.0(bioc 3.24)GEOmetadb-1.74.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructure

6.57 score 247 scripts 645 downloads 27 mentions 4 exports 18 dependencies

Last updated from:28688e04f4. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR140
linux-devel-x86_64WARNING214
source / vignettesOK199
linux-release-x86_64WARNING170
macos-release-arm64WARNING86
macos-oldrel-arm64WARNING84
windows-develWARNING94
windows-releaseWARNING106
windows-oldrelWARNING90
wasm-releaseOK116

Exports:columnDescriptionsgeoConvertgetBiocPlatformMapgetSQLiteFile

Dependencies:bitbit64blobcachemclicpp11DBIfastmapgluelifecyclememoisepkgconfigR.methodsS3R.ooR.utilsrlangRSQLitevctrs

Using the GEOmetadb Package

Jack Zhu and Sean Davis

Rendered fromGEOmetadb.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-24
Started: 2014-09-21