R Observatory: Metrics for randomGODB version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

randomGODB

1.1

Random GO Database

4packages depend

3.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2025-05-072 releasesCRAN page ↗

The Gene Ontology (GO) Consortium https://geneontology.org/ organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) doi:10.1186/gb-2003-4-4-r28) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. The significance is traditionally determined by randomizing the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for each category. We explore here the novel alternative of randomizing the GO database rather than the gene list.

Install

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

install.packages("randomGODB", 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-randomgodb

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-randomGODB

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-randomGODB

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

Health

CRAN checks

13OK

Slowest check: 1.3 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

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 3 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 17%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #22,259 · ~10/day · ~291/mo

Releases R versions

Daily download trend is not available in this view yet.

12430 days

48690 days

3.5K1 year

Compare downloads with other packages →

Also on134 r2u21 autocran

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (3)

minimalistGODBgraphicsstats

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat GO.db

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

1indirect

GoMiner HTGM2D HTGM3D HTGM4D

Code & Tests

People & History

People (1)

Maintainer (1)

Barry Zeeberg

Author, Maintainer

Authors (1)

Barry Zeeberg

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1Latest
2026-01-10 · current release · diff ↗
1.0
2025-05-07
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-07
Total releases: 2 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Download size: 829 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("randomGODB")

Format

Zeeberg, B. (2026). randomGODB: Random GO Database (Version 1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.randomGODB

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 randomGODB version 1.1 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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