HTGM3D

1.0.3

Three Dimensional High Throughput 'GoMiner'

0packages depend

17Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2025-05-304 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. 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.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-09
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 70%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

17K

CRAN downloads in the past year

Rank #8,495 · ~47/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

1.3K90 days

17K1 year

Compare downloads with other packages →

Also on140 r2u

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Barry Zeeberg

Author, Maintainer

Authors (1)

Barry Zeeberg

Author, Maintainer

Package Timeline

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

1.0.3Latest
2026-04-26 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.2
2026-02-20 · diff ↗
1.0.1
2026-02-08 · diff ↗
unarchivedReturned to CRAN
2026-02-08
archivedRemoved from CRAN
2026-02-01
requires archived package 'HTGM2D'
1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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