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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.
| Version: | 1.1 |
| Depends: | R (≥ 4.2.0) |
| Imports: | minimalistGODB, GoMiner, grDevices, stats, gplots |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2025-04-05 |
| DOI: | 10.32614/CRAN.package.HTGM |
| 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: | HTGM results |
| Reference manual: | HTGM.pdf |
| Vignettes: |
High Throughput GoMiner (HTGM) (source) |
| Package source: | HTGM_1.1.tar.gz |
| Windows binaries: | r-devel: HTGM_1.1.zip, r-release: HTGM_1.1.zip, r-oldrel: HTGM_1.1.zip |
| macOS binaries: | r-release (arm64): HTGM_1.1.tgz, r-oldrel (arm64): HTGM_1.1.tgz, r-release (x86_64): HTGM_1.1.tgz, r-oldrel (x86_64): HTGM_1.1.tgz |
| Old sources: | HTGM archive |
| Reverse imports: | HTGM2D |
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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.