HTGM2D: Two Dimensional High Throughput 'GoMiner'

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.

Version:	1.0
Depends:	R (≥ 4.2.0)
Imports:	minimalistGODB, GoMiner, HTGM, grDevices, stats, gplots, jaccard
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2025-04-07
DOI:	10.32614/CRAN.package.HTGM2D
Author:	Barry Zeeberg [aut, cre]
Maintainer:	Barry Zeeberg <barryz2013 at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
CRAN checks:	HTGM2D results

Documentation:

Reference manual:	HTGM2D.pdf
Vignettes:	Two Dimensional High Throughput GoMiner (HTGM2D) (source)

Downloads:

Package source:	HTGM2D_1.0.tar.gz
Windows binaries:	r-devel: HTGM2D_1.0.zip, r-release: HTGM2D_1.0.zip, r-oldrel: HTGM2D_1.0.zip
macOS binaries:	r-devel (arm64): HTGM2D_1.0.tgz, r-release (arm64): HTGM2D_1.0.tgz, r-oldrel (arm64): HTGM2D_1.0.tgz, r-devel (x86_64): HTGM2D_1.0.tgz, r-release (x86_64): HTGM2D_1.0.tgz, r-oldrel (x86_64): HTGM2D_1.0.tgz

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