Package: TaxSEA
Type: Package
Title: Taxon Set Enrichment Analysis
Version: 1.4.0
Authors@R: c(person("Feargal", "Ryan", 
    email = "feargalr@gmail.com", 
    role = c("aut", "cre","fnd"),comment = c(ORCID = "0000-0002-1565-4598",
                      funding = "Supported by NHMRC Investigator Grant")))
Description: TaxSEA is an R package for Taxon Set Enrichment Analysis, which 
    utilises a Kolmogorov-Smirnov test analyses to 
    investigate differential abundance analysis output for whether there
    are alternations in a-priori defined sets of taxa from  
    public databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, BacDive and
    GMRepoV2) and collated from the literature.  
    TaxSEA takes as input a list of taxonomic identifiers (e.g. species names, 
    NCBI IDs etc.) and a rank (E.g. fold change, correlation coefficient). 
    TaxSEA be applied to any microbiota taxonomic profiling technology 
    (array-based, 16S rRNA gene sequencing, shotgun metagenomics & 
    metatranscriptomics etc.) and enables researchers to rapidly contextualize 
    their findings within the broader literature to accelerate interpretation 
    of results.
License: GPL-3
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
RoxygenNote: 7.3.3
biocViews: Microbiome, Metagenomics, Sequencing, GeneSetEnrichment,
        RNASeq
URL: https://github.com/feargalr/taxsea,
        https://feargalr.github.io/TaxSEA/
BugReports: https://github.com/feargalr/taxsea/issues
Depends: R (>= 4.5.0)
Suggests: BiocStyle, bugsigdbr, fgsea, knitr, mia, rmarkdown,
        SummarizedExperiment, testthat
Imports: stats, utils
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/TaxSEA
git_branch: RELEASE_3_23
git_last_commit: 76ffa27
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 23:43:24 UTC; biocbuild
Author: Feargal Ryan [aut, cre, fnd] (ORCID:
    <https://orcid.org/0000-0002-1565-4598>, funding: Supported by
    NHMRC Investigator Grant)
Maintainer: Feargal Ryan <feargalr@gmail.com>
Built: R 4.6.0; ; 2026-04-29 05:03:29 UTC; unix
