randomGODB: Random GO Database

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. The significance is traditionally determined by randomizing the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for each category. We explore here the novel alternative of randomizing the GO database rather than the gene list.

Version:	1.0
Depends:	R (≥ 4.2.0)
Imports:	minimalistGODB, GO.db, graphics, stats
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2025-05-07
DOI:	10.32614/CRAN.package.randomGODB
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:	randomGODB results

Documentation:

Reference manual:	randomGODB.pdf
Vignettes:	Random GO Database (source)

Downloads:

Package source:	randomGODB_1.0.tar.gz
Windows binaries:	r-devel: randomGODB_1.0.zip, r-release: randomGODB_1.0.zip, r-oldrel: randomGODB_1.0.zip
macOS binaries:	r-release (arm64): randomGODB_1.0.tgz, r-oldrel (arm64): randomGODB_1.0.tgz, r-release (x86_64): randomGODB_1.0.tgz, r-oldrel (x86_64): randomGODB_1.0.tgz

Reverse dependencies:

Reverse imports:

GoMiner, HTGM2D, HTGM3D

Linking:

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