R Observatory: Metrics for geneExpressionFromGEO version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

geneExpressionFromGEO

1.3Package record

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

0packages depend

4.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Davide ChiccoCRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (1)

geneExpressionFromGEOvignette HTML

How these are measured

Downloads

4.5K

CRAN downloads in the past year

Rank #8,882 · ~12/day · ~374/mo

Releases R versions

Daily download trend is not available in this view yet.

40630 days

1.1K90 days

4.5K1 year

Compare downloads with other packages →

Also on108 r2u601 bioconda29 c2d4u

How downloads are counted

Repository

davidechicco/geneexpressionfromgeo ↗Account: davidechicco

6Stars

2Forks

2Open issues

0Open PRs

0Releases

34Commits

1Commit identities

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

Responsiveness

not measured

Stars over time

2023-11-29 · 62026-07-07 · 6

How these are measured

PracticesBeta

Checks run against github.com/davidechicco/geneexpressionfromgeo on 2026-10-21.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing geneExpressionFromGEO adds 3 packages (3 with compiled code, 1.5 MB of source tarballs). Heaviest: rlang 766 KB, cli 629 KB, xml2 152 KB. 3 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

People & History

People (1)

Davide Chicco

Author, Maintainer since 0.2 (2020)

Releases (9)

Pick two releases to compare their code metrics.

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

Show 1 earlier eventHide 1 earlier event

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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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