Package: TaxSEA
Type: Package
Title: Taxon Set Enrichment Analysis
Version: 1.5.5
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
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, S4Vectors, bugsigdbr, fgsea, knitr, mia,
        rmarkdown, SummarizedExperiment, testthat
Imports: methods, stats, utils
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-17 08:27:43 UTC
RemoteUrl: https://github.com/bioc/TaxSEA
RemoteRef: HEAD
RemoteSha: 15c9b9ea2d8b3255f8cfbf8226bb5fb9270bd74e
NeedsCompilation: no
Packaged: 2026-09-17 13:43:50 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 4.6.1; ; 2026-09-17 13:45:31 UTC; windows
