Software & methodsBioconductor

TaxSEA

Taxon set enrichment analysis for microbiome data

BiocManager::install("TaxSEA")

Differential abundance analysis produces long lists of taxa that went up or down, which are hard to interpret one by one. TaxSEA asks what those taxa have in common. It tests whether predefined sets of taxa (published disease signatures from BugSigDB, producers of specific metabolites from MiMeDB, and other curated collections) are shifted as a group, using a Kolmogorov-Smirnov test on the ranked fold changes. It works with the output of DESeq2, ALDEx2, MaAsLin2, ANCOM-BC or any other method that gives a fold change per taxon.

How to cite TaxSEA

Ryan FJ et al. TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases. Briefings in Bioinformatics. 2025. doi:10.1093/bib/bbaf173

@article{ryan2025taxsea,
  title   = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases},
  author  = {Ryan, Feargal J. and others},
  journal = {Briefings in Bioinformatics},
  year    = {2025},
  doi     = {10.1093/bib/bbaf173}
}