R Observatory: Metrics for HTGM4D version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTGM4D

1.0

Four Dimensional High Throughput 'GoMiner'

0packages depend

1.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2026-05-021 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. Microarray studies are usually analyzed with BP, whereas proteomics researchers often prefer CC. To capture the benefit of both of those ontologies, I now present an enhancement of the existing two-dimensional version of 'High-Throughput GoMiner' ('HTGM2D'), which is called 'HTGM4D'. The original 'HTGM2D' is augmented by adding two instances of the original 'GoMiner' genes versus categories heatmaps, aligned with the categories axes of the 'HTGM2D' heatmap.

Install

R (CRAN)Ubuntu (r2u)

install.packages("HTGM4D", 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-htgm4d

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

Health

CRAN checks

13OK

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

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
OK2026-05-03
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 44%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.3K

CRAN downloads in the past year

Rank #10,370 · ~4/day · ~109/mo

Releases R versions

Daily download trend is not available in this view yet.

20130 days

92090 days

1.3K1 year

Compare downloads with other packages →

Also on25 r2u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (15)

minimalistGODB GoMiner HTGM HTGM2DgrDevicesstatsgplots vprint randomGODB HGNChelper png magick svgliteutilsgraphics

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Barry Zeeberg

Author, Maintainer

Authors (1)

Barry Zeeberg

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

1.0Latest
2026-05-02 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-02
Total releases: 1 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 30 KB / 7 files
Download size: 3.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HTGM4D")

Format

Zeeberg, B. (2026). HTGM4D: Four Dimensional High Throughput 'GoMiner' (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.HTGM4D

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 HTGM4D version 1.0 [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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