R Observatory: Metrics for geneExpressionFromGEO version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

geneExpressionFromGEO

1.3

Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets

0packages depend

4.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Davide ChiccoFirst published 2020-11-169 releasesCRAN page ↗GitHub ↗

A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL https://ftp.ncbi.nlm.nih.gov/geo/series/. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, doi:10.1007/978-1-0716-1839-4_12.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("geneExpressionFromGEO", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("davidechicco/geneExpressionFromGEO")

Development version from davidechicco/geneExpressionFromGEO. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-geneexpressionfromgeo

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

4.3K

CRAN downloads in the past year

Rank #11,634 · ~12/day · ~361/mo

Releases R versions

Daily download trend is not available in this view yet.

20530 days

84490 days

4.3K1 year

Compare downloads with other packages →

Also on134 r2u535 bioconda8 c2d4u

Repository

GitHub ↗ davidechicco/geneexpressionfromgeo

6Stars

2Forks

2Open issues

0Open PRs

0Releases

34Commits

1Contributors

License GPL-3.0 · 34 commits · Last activity 2025-10-17

Stars over time

2023-11-29 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

Checks run against github.com/davidechicco/geneexpressionfromgeo on 2026-08-16.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (5)

xml2 Biobase annotate GEOqueryutils

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Davide Chicco

Author, Maintainer

Authors (1)

Davide Chicco

Author, Maintainer

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.3Latest
2025-12-09 · current release · diff ↗
1.2
2025-04-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.9
2021-12-16 · diff ↗
0.8
2021-11-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.6
2021-04-24 · diff ↗
0.5
2021-04-06 · diff ↗
archivedRemoved from CRAN
2021-02-21
policy violation On Internet access
0.4
2021-01-25 · diff ↗
0.3
2020-11-17 · diff ↗
0.2
2020-11-16

Show 1 earlier events

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-16
Total releases: 9 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 9.5 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("geneExpressionFromGEO")

Format

Chicco, D. (2025). geneExpressionFromGEO: Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets (Version 1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.geneExpressionFromGEO

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for geneExpressionFromGEO version 1.3 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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