R Observatory: Metrics for HTGM2D version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTGM2D

1.1.1Package record

Two Dimensional High Throughput 'GoMiner'

2packages depend

4Kdownloads / 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 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. 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: 2.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 67%4 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Two Dimensional High Throughput GoMiner (HTGM2D) HTML

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #17,687 · ~11/day · ~332/mo

Releases R versions

Daily download trend is not available in this view yet.

25230 days

73190 days

4K1 year

Compare downloads with other packages →

Also on97 r2u

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing HTGM2D adds 47 packages (26 with compiled code, 58 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 (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

Imports 2

Depends, Imports or LinkingTo, most downloaded first

HTGM3D HTGM4D

How these are counted

Code & Tests

Datasets

People & History

People (1)

Barry Zeeberg

Author, Maintainer since 1.0 (2025)

Releases (3)

Pick two releases to compare their code metrics.

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

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 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 HTGM2D version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →