Package: GOfuncR
Type: Package
Title: Gene ontology enrichment using FUNC
Version: 1.20.0
Date: 2021-08-29
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: 2023-04-25 21:19:26 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/GOfuncR
git_branch: RELEASE_3_17
git_last_commit: 2374d68
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Built: R 4.3.1; aarch64-conda-linux-gnu; 2023-09-02 04:03:53 UTC; unix
