# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "TaxSEA" in publications use:'
type: software
license: GPL-3.0-only
title: 'TaxSEA: Taxon Set Enrichment Analysis'
version: 1.5.0
doi: 10.1093/bib/bbaf173
identifiers:
- type: doi
  value: 10.32614/CRAN.package.TaxSEA
abstract: 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.
authors:
- family-names: Ryan
  given-names: Feargal
  email: feargalr@gmail.com
  orcid: https://orcid.org/0000-0002-1565-4598
preferred-citation:
  type: article
  title: 'TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment
    analysis and public databases'
  authors:
  - family-names: Pham
    given-names: Cong M
  - family-names: Rankin
    given-names: Timothy J
  - family-names: Stinear
    given-names: Timothy P
  - family-names: Walsh
    given-names: Calum J
  - family-names: Ryan
    given-names: Feargal J
  journal: Briefings in Bioinformatics
  year: '2025'
  volume: Volume 26, Issue 2
  doi: 10.1093/bib/bbaf173
  url: https://doi.org/10.1093/bib/bbaf173
repository: https://bioc.r-universe.dev
repository-code: https://github.com/feargalr/taxsea
commit: ae582a26297f236feb1584848c75994be24b3a84
url: https://feargalr.github.io/TaxSEA/
date-released: '2026-04-28'
contact:
- family-names: Ryan
  given-names: Feargal
  email: feargalr@gmail.com
  orcid: https://orcid.org/0000-0002-1565-4598