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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 now present an enhancement of the existing two-dimensional version of 'High-Throughput GoMiner' ('HTGM2D'), which is called 'HTGM4D'. The original 'HTGM2D' is augmented by adding two instances of the original 'GoMiner' genes versus categories heatmaps, aligned with the categories axes of the 'HTGM2D' heatmap.
| Version: | 1.0 |
| Depends: | R (≥ 4.2.0) |
| Imports: | minimalistGODB, GoMiner, HTGM, HTGM2D, grDevices, stats, gplots, vprint, randomGODB, HGNChelper, png, magick, svglite, utils, graphics |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2026-05-02 |
| DOI: | 10.32614/CRAN.package.HTGM4D |
| 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: | HTGM4D results |
| Reference manual: | HTGM4D.html , HTGM4D.pdf |
| Vignettes: |
Four Dimensional High Throughput GoMiner (HTGM4D) (source) |
| Package source: | HTGM4D_1.0.tar.gz |
| Windows binaries: | r-devel: HTGM4D_1.0.zip, r-release: HTGM4D_1.0.zip, r-oldrel: HTGM4D_1.0.zip |
| macOS binaries: | r-release (arm64): HTGM4D_1.0.tgz, r-oldrel (arm64): HTGM4D_1.0.tgz, r-release (x86_64): HTGM4D_1.0.tgz, r-oldrel (x86_64): HTGM4D_1.0.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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