R Observatory: Metrics for GoMiner version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GoMiner

1.3

Automate the Mapping Between a List of Genes and Gene Ontology Categories

4packages depend

6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2025-03-254 releasesCRAN page ↗

In gene-expression microarray studies, for example, one generally obtains a list of dozens or hundreds of genes that differ in expression between samples and then asks 'What does all of this mean biologically?' Alternatively, gene lists can be derived conceptually in addition to experimentally. For instance, one might want to analyze a group of genes known as housekeeping genes. The work of the Gene Ontology (GO) Consortium <geneontology.org> provides a way to address that question. GO organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. The role of 'GoMiner' is to automate the mapping between a list of genes and GO, and to provide a statistical summary of the results as well as a visualization.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

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-gominer

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-GoMiner

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-GoMiner

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

8

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 24%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6K

CRAN downloads in the past year

Rank #7,339 · ~17/day · ~502/mo

Releases R versions

Daily download trend is not available in this view yet.

13230 days

1.2K90 days

6K1 year

Compare downloads with other packages →

Also on187 r2u10 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (8)

minimalistGODB HGNChelper randomGODBstatsgplotsgrDevicesutilsvprint

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

HTGM HTGM2D HTGM3D HTGM4D

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Barry Zeeberg

Author, Maintainer

Authors (1)

Barry Zeeberg

Author, Maintainer

Package Timeline

4 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
2025-06-06 · current release · diff ↗
1.2
2025-05-18 · diff ↗
1.1
2025-05-14 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0
2025-03-25
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-25
Total releases: 4 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 2.6 MB / 12 files
Download size: 3.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GoMiner")

Format

Zeeberg, B. (2025). GoMiner: Automate the Mapping Between a List of Genes and Gene Ontology Categories (Version 1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.GoMiner

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 GoMiner version 1.3 [Data set]. HJJB, LLC. Data release v2026-08-08. https://doi.org/10.5281/zenodo.21843040

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

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