Package: TaxSEA
Type: Package
Title: Taxon Set Enrichment Analysis
Version: 1.3.3
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 (>= 4.4.0)
Suggests: BiocStyle, bugsigdbr, fgsea, knitr, mia, rmarkdown,
        SummarizedExperiment, testthat
Imports: stats, utils
Config/testthat/edition: 3
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-02-12 00:34:21 UTC
RemoteUrl: https://github.com/bioc/TaxSEA
RemoteRef: HEAD
RemoteSha: e31549895e5548b48cde5f685a7ee4efeb4138e4
NeedsCompilation: no
Packaged: 2026-03-16 08:45:47 UTC; root
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; ; 2026-03-16 08:47:14 UTC; windows
