R Observatory: Metrics for randomGODB version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

randomGODB

1.1Package record

Random GO Database

4packages depend

3.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Barry ZeebergCRAN 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. 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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.3 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 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12
Examples that run: 17%2 run in a plain check (1 of them under a condition) · 10 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Random GO Database HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #23,103 · ~8/day · ~256/mo

Releases R versions

Daily download trend is not available in this view yet.

21130 days

56490 days

3.1K1 year

Compare downloads with other packages →

Also on104 r2u1 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing randomGODB adds 1 package (0 with compiled code, 2.1 MB of source tarballs). Heaviest: minimalistGODB 2.1 MB.

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

Imports 4

Depends, Imports or LinkingTo, most downloaded first

GoMiner HTGM3D HTGM4D HTGM2D

How these are counted

Code & Tests

People & History

People (1)

Barry Zeeberg

Author, Maintainer since 1.0 (2025)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1Latest
record
2026-01-10 · current release · diff ↗
1.0
record
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

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 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 randomGODB version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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