R Observatory: Metrics for HTGM4D version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTGM4D

1.0Package record

Four Dimensional High Throughput 'GoMiner'

0packages depend

1.9Kdownloads / 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. 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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-05-03

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 25
Examples that run: 44%7 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 5 never run
Exported functions with examples: 89%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Four Dimensional High Throughput GoMiner (HTGM4D) HTML

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #16,819 · ~5/day · ~162/mo

Releases R versions

Daily download trend is not available in this view yet.

23430 days

76090 days

1.9K1 year

Compare downloads with other packages →

Also on30 r2u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing HTGM4D adds 55 packages (32 with compiled code, 65 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, bslib 5.6 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Barry Zeeberg

Author, Maintainer since 1.0 (2026)

Releases (1)

1.0Latest
record
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

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 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 HTGM4D version 1.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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