Package: GOfuncR
Type: Package
Title: Gene ontology enrichment using FUNC
Version: 1.31.0
Date: 2024-02-03
Author: Steffi Grote
Maintainer: Steffi Grote <grote.steffi@gmail.com>
Description: GOfuncR performs a gene ontology enrichment analysis based
        on the ontology enrichment software FUNC. GO-annotations are
        obtained from OrganismDb or OrgDb packages ('Homo.sapiens' by
        default); the GO-graph is included in the package and updated
        regularly (01-May-2021). GOfuncR provides the standard
        candidate vs. background enrichment analysis using the
        hypergeometric test, as well as three additional tests: (i) the
        Wilcoxon rank-sum test that is used when genes are ranked, (ii)
        a binomial test that is used when genes are associated with two
        counts and (iii) a Chi-square or Fisher's exact test that is
        used in cases when genes are associated with four counts. To
        correct for multiple testing and interdependency of the tests,
        family-wise error rates are computed based on random
        permutations of the gene-associated variables. GOfuncR also
        provides tools for exploring the ontology graph and the
        annotations, and options to take gene-length or spatial
        clustering of genes into account. It is also possible to
        provide custom gene coordinates, annotations and ontologies.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
        GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
        grDevices, graphics, stats,
Depends: R (>= 3.4), vioplot (>= 0.2),
LinkingTo: Rcpp
Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
VignetteBuilder: knitr
biocViews: GeneSetEnrichment, GO
NeedsCompilation: yes
Packaged: 2025-11-02 14:58:37 UTC; root
Config/pak/sysreqs: libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:42:27 UTC
RemoteUrl: https://github.com/bioc/GOfuncR
RemoteRef: HEAD
RemoteSha: 781f3d4e35f89f1798226412528f85a682a86bf9
Built: R 4.6.0; x86_64-w64-mingw32; 2025-11-02 15:02:34 UTC; windows
Archs: x64
