R Observatory: Metrics for HTGM3D version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTGM3D

1.0.3Package record

Three Dimensional High Throughput 'GoMiner'

0packages depend

16.6Kdownloads / 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. To capture the benefit of all three ontologies, I developed 'HTGM3D', a three-dimensional version of 'GoMiner'.

Install

R (CRAN)Ubuntu (r2u)

install.packages("HTGM3D", 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-htgm3d

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: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 3 earlier changesHide 3 earlier changes

WARNING12 OK, 1 WARNING2026-05-09
OK12 OK2026-04-25
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 20
Examples that run: 70%7 run in a plain check (1 of them under a condition) · 3 never run
Exported functions with examples: 77%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Three Dimensional High Throughput GoMiner (HTGM3D) HTML

How these are measured

Downloads

16.6K

CRAN downloads in the past year

Rank #12,391 · ~45/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

32030 days

89390 days

16.6K1 year

Compare downloads with other packages →

Also on100 r2u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing HTGM3D adds 90 packages (49 with compiled code, 92 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, data.table 5.7 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.2.0

Imports (12)

minimalistGODB GoMiner HTGM HTGM2DgrDevicesstatsR2HTML rgl vprint randomGODB stringr salesforcer

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 (2025)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.3Latest
record
2026-02-20 · current release · diff ↗
1.0.2
record
2026-02-20 · diff ↗
unarchivedReturned to CRAN
2026-02-08
1.0.1
record
2026-02-08 · diff ↗ ·
added 1 export
whichOS
archivedRemoved from CRAN
2026-02-01
requires archived package 'HTGM2D'
1.0
record
2025-05-30
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-30
Total releases: 4 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 251 KB / 7 files
Download size: 2.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HTGM3D")

Format

Zeeberg, B. (2026). HTGM3D: Three Dimensional High Throughput 'GoMiner' (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.HTGM3D

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 HTGM3D version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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