HTGM

1.2

High Throughput 'GoMiner'

3packages depend

6.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Barry ZeebergFirst published 2025-04-023 releasesCRAN page ↗

Two papers published in the early 2000's (Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) doi:10.1186/gb-2003-4-4-r28) and (Zeeberg, B.R., Qin, H., Narashimhan, S., et al. (2005) doi:10.1186/1471-2105-6-168) implement 'GoMiner' and 'High Throughput GoMiner' ('HTGM') to map lists of genes to the Gene Ontology (GO) https://geneontology.org. Until recently, these were hosted on a server at The National Cancer Institute (NCI). In order to continue providing these services to the bio-medical community, I have developed stand-alone versions. The current package 'HTGM' builds upon my recent package 'GoMiner'. The output of 'GoMiner' is a heatmap showing the relationship of a single list of genes and the significant categories into which they map. 'High Throughput GoMiner' ('HTGM') integrates the results of the individual 'GoMiner' analyses. The output of 'HTGM' is a heatmap showing the relationship of the significant categories derived from each gene list. The heatmap has only 2 axes, so the identity of the genes are unfortunately "integrated out of the equation." Because the graphic for the heatmap is implemented in Scalable Vector Graphics (SVG) technology, it is relatively easy to hyperlink each picture element to the relevant list of genes. By clicking on the desired picture element, the user can recover the "lost" genes.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("HTGM", 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-htgm

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-HTGM

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-HTGM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.5 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6.3K

CRAN downloads in the past year

Rank #7,063 · ~17/day · ~522/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

1.4K90 days

6.3K1 year

Compare downloads with other packages →

Also on116 r2u44 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (6)

minimalistGODB GoMinergrDevicesstatsgplots vprint

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

HTGM2D 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
1.2Latest
2025-05-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1
2025-04-05 · diff ↗
1.0
2025-04-02
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-04-02
Total releases: 3 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 233 KB / 9 files
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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