Package: TaxSEA
Type: Package
Title: Taxon Set Enrichment Analysis
Version: 1.5.8
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 makes metagenomic data easier to interpret. Rather
        than reading species one at a time, it tests whether a-priori
        defined sets of taxa shift together, drawing on public
        databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, BacDive and
        GMRepoV2) and on sets collated from the literature. Two
        approaches are provided. TaxSEA takes taxon names or NCBI IDs
        with a rank per taxon, such as a fold change or correlation
        coefficient, and tests each set with a Kolmogorov-Smirnov test.
        ssTaxSEA scores every set in a single sample as the mean
        centered log-ratio of its members, giving a per-sample value to
        use in any downstream model. Both work with any taxonomic
        profiling technology, including 16S rRNA gene sequencing,
        shotgun metagenomics and metatranscriptomics.
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: 2026-10-26 06:37:55 UTC
RemoteUrl: https://github.com/bioc/TaxSEA
RemoteRef: HEAD
RemoteSha: 9831356494cf3096773098dea7216393db07dffb
NeedsCompilation: no
Packaged: 2026-10-26 23:27:41 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>