R Observatory: Metrics for HTGM2D version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTGM2D

1.1.1

Two Dimensional High Throughput 'GoMiner'

2packages depend

4.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2025-04-073 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 developed a two-dimensional version of 'High-Throughput GoMiner' ('HTGM2D'). I generate a 2D heat map whose axes are any two of BP, MF, or CC, and the value within a picture element of the heat map reflects the Jaccard metric p-value for the number of genes in common for the corresponding pair.

Install

R (CRAN)Ubuntu (r2u)

install.packages("HTGM2D", 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-htgm2d

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

10

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.4K

CRAN downloads in the past year

Rank #16,981 · ~12/day · ~367/mo

Releases R versions

Daily download trend is not available in this view yet.

13530 days

62990 days

4.4K1 year

Compare downloads with other packages →

Also on128 r2u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (10)

minimalistGODB GoMiner HTGMgrDevicesstatsgplots jaccard vprint randomGODB HGNChelper

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

HTGM3D HTGM4D

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Barry Zeeberg

Author, Maintainer

Authors (1)

Barry Zeeberg

Author, Maintainer

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.1Latest
2026-02-04 · current release · diff ↗
unarchivedReturned to CRAN
2026-02-03
archivedRemoved from CRAN
2026-02-01
requires archived package 'jaccard'
1.1
2025-05-18 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0
2025-04-07
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-04-07
Total releases: 3 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 280 KB / 8 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HTGM2D")

Format

Zeeberg, B. (2026). HTGM2D: Two Dimensional High Throughput 'GoMiner' (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.HTGM2D

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 HTGM2D version 1.1.1 [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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