minimalistGODB

1.1.0

Build a Minimalist Gene Ontology (GO) Database (GODB)

6packages depend

6.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2025-03-182 releasesCRAN page ↗

Normally building a GODB is fairly complicated, involving downloading multiple database files and using these to build e.g. a 'mySQL' database. Accessing this database is also complicated, involving an intimate knowledge of the database in order to construct reliable queries. Here we have a more modest goal, generating GOGOA3, which is a stripped down version of the GODB that was originally restricted to human genes as designated by the HUGO Gene Nomenclature Committee (HGNC) (see https://geneontology.org/). I have now added about two dozen additional species, namely all species represented on the Gene Ontology download page https://current.geneontology.org/products/pages/downloads.html. This covers most of the model organisms that are commonly used in bio-medical and basic research (assuming that anyone still has a grant to do such research). This can be built in a matter of seconds from 2 easily downloaded files (see https://current.geneontology.org/products/pages/downloads.html and https://geneontology.org/docs/download-ontology/), and it can be queried by e.g. w<-which(GOGOA3[,"HGNC"] %in% hgncList) where GOGOA3 is a matrix representing the minimalist GODB and hgncList is a list of gene identifiers. This database will be used in my upcoming package 'GoMiner' which is based on my previous publication (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003)doi:10.1186/gb-2003-4-4-r28). Relevant .RData files are available from GitHub (https://github.com/barryzee/GO/tree/main/databases).

Install

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

install.packages("minimalistGODB", 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-minimalistgodb

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

# 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-minimalistGODB

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

Health

CRAN checks

13OK

Slowest check: 1.6 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-08
12 OK · 0 NOTE · 1 WARNING · 0 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: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6.3K

CRAN downloads in the past year

Rank #7,282 · ~17/day · ~523/mo

Releases R versions

Daily download trend is not available in this view yet.

29530 days

1.4K90 days

6.3K1 year

Compare downloads with other packages →

Also on135 r2u27 autocran

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (0)

none

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

GoMiner HTGM HTGM2D HTGM3D HTGM4D randomGODB

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
1.1.0Latest
2025-05-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0
2025-03-18
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-18
Total releases: 2 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 1.1 MB / 3 files
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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