Package: TaxSEA 1.5.8

Feargal Ryan

TaxSEA: Taxon Set Enrichment Analysis

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.

Authors:Feargal Ryan [aut, cre, fnd]

TaxSEA_1.5.8.tar.gz
TaxSEA_1.5.8.zip(r-4.7-any)TaxSEA_1.5.8.zip(r-4.6-any)TaxSEA_1.5.8.zip(r-4.5-any)
TaxSEA_1.5.8.tgz(r-4.6-any)TaxSEA_1.5.8.tgz(r-4.5-any)
TaxSEA_1.5.8.tar.gz(r-4.7-any)TaxSEA_1.5.8.tar.gz(r-4.6-any)
TaxSEA_1.5.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TaxSEA/json (API)

# Install 'TaxSEA' in R:
install.packages('TaxSEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/feargalr/taxsea/issues

Pkgdown/docs site:https://feargalr.github.io

Datasets:
  • NCBI_ids - NCBI IDs Dataset
  • TaxSEA_db - TaxSEA Database A dataset containing taxon sets. Each item in the list is a taxon set, and each member within a taxon set is a taxon.
  • TaxSEA_test_data - TaxSEA Test Data

On BioConductor:TaxSEA-1.5.7(bioc 3.24)TaxSEA-1.4.0(bioc 3.23)

microbiomemetagenomicssequencinggenesetenrichmentrnaseq

6.48 score 12 stars 14 scripts 322 downloads 5 exports 0 dependencies

Last updated from:9831356494. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING223
linux-develOK296
source / vignettesOK322
linux-releaseOK308
macos-releaseOK168
macos-oldrelOK153
windows-develOK173
windows-releaseOK131
windows-oldrelOK107
wasm-releaseOK120

Exports:get_ncbi_taxon_idsget_taxon_setsssTaxSEAtaxon_rank_setsTaxSEA

Dependencies:

Single-sample enrichment with ssTaxSEA
Why per-person enrichment? | How it works | Usage | From a count matrix | A single sample | With the built-in database | From a TreeSummarizedExperiment | Interpreting the scores | Practical considerations | When to use ssTaxSEA vs TaxSEA | Downstream analysis
Rendered fromsingle-sample-enrichment.Rmdusingknitr::rmarkdown

Last update: 2026-10-26
Started: 2026-02-12

TaxSEA
TaxSEA: Taxon Set Enrichment Analysis | Installation | Taxon set database | Test data | Functions | Usage | Retrieve sets containing a particular taxon | Running an enrichment analysis | Run TaxSEA with test data | Output | BugSigDB | TaxSEA database with other enrichment tools
Rendered fromTaxSEA.Rmdusingknitr::rmarkdown

Last update: 2026-09-21
Started: 2024-12-09

Testing higher taxonomic levels without collapsing your data
Rendered fromTaxonomic-aggregation.Rmdusingknitr::rmarkdown

Last update: 2026-02-10
Started: 2026-01-13

Why use taxon set enrichment analysis?
The challenge with interpreting differences in microbiome data | The idea behind Taxon Set Enrichment Analysis | But isn’t this what functional profiling tools (e.g. HUMAnN3) do?
Rendered fromwhy-taxon-set-enrichment.Rmdusingknitr::rmarkdown

Last update: 2026-01-15
Started: 2026-01-13

Analysis types
ORA vs Enrichment (two ways to run TaxSEA) | Enrichment (rank-based) | What it does (in plain terms) | When to use it (recommended in most cases) | Pros | Cons | ORA (Over-Representation Analysis) | When to use it | Recommended practice
Rendered fromORA_vs_ES.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2026-01-14

Frequently Asked Questions
What problem does TaxSEA actually solve? | Is TaxSEA a replacement for differential abundance? | Can I use TaxSEA even when there are no individual species level differences? | How is this different from functional profiling tools like HUMAnN3? | Does this only work for the human gut microbiome? | Do I need differential abundance results first? | Why use ranks instead of thresholds? | Isn’t this just gene set enrichment, but for microbes? | Will this work if my DA results are messy or inconsistent? | Have you shown TaxSEA is accurate? | When should I not use TaxSEA? | Can I use TaxSEA with 16S rRNA gene sequencing data? | Why does TaxSEA use species-level data instead of strain-level?
Rendered fromFAQs.Rmdusingknitr::rmarkdown

Last update: 2026-01-13
Started: 2026-01-13