GEOquery
Bioc currentGet data from NCBI Gene Expression Omnibus (GEO)
Release Lineage
Entered 1.8 · Apr 27, 2006
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
55 17 exported
Complexity
3 avg / 11 max
Call network
55 nodes / 62 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
3,963
Files
72
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
38
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.18
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
5.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
41
First release
2006-09-07
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
22
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 33 (9 internal)
- Examples that run
- 67%10 run in a plain check · 4 never run · 1 hold no code
- Exported functions with examples
- 94%
- Documented parameters
- 100%
- Return-value docs
- 81%
- Help pages citing references
- 6%
- GEOquery.html HTML
- single-cell.html HTML
Repository practices
14 development-tooling and community-health practices detected across 6 families in the upstream repository
Checks run against github.com/seandavi/geoquery on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-08-17 · The repository has a site deploy workflow
pkgdown site last built 2026-08-17
Show all practicesHide 2 practices
Datasets
Topics
Depended on by (28)
Show 58 packagesHide 58 packages
Bioconductor (26)
CRAN (2)
Suggested by (63)
People
- Sean Davis author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("GEOquery")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btm254.
The repository also keeps a CITATION.cff.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.