Package: GOfuncR
Type: Package
Title: Gene ontology enrichment using FUNC
Version: 1.28.0
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: 2025-04-16 01:13:40 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/GOfuncR
git_branch: RELEASE_3_21
git_last_commit: dc85544
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:35:38 UTC; windows
Archs: x64
