Package: TaxSEA 1.5.0

Feargal Ryan

TaxSEA: Taxon Set Enrichment Analysis

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:Feargal Ryan [aut, cre, fnd]

TaxSEA_1.5.0.tar.gz
TaxSEA_1.5.0.zip(r-4.7)TaxSEA_1.5.0.zip(r-4.6)TaxSEA_1.5.0.zip(r-4.5)
TaxSEA_1.5.0.tgz(r-4.6-any)TaxSEA_1.5.0.tgz(r-4.5-any)
TaxSEA_1.5.0.tar.gz(r-4.7-any)TaxSEA_1.5.0.tar.gz(r-4.6-any)
TaxSEA_1.5.0.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-1.5.0(bioc 3.24)TaxSEA-1.4.0(bioc 3.23)

microbiomemetagenomicssequencinggenesetenrichmentrnaseq

6.48 score 10 stars 7 scripts 246 downloads 5 exports 0 dependencies

Last updated from:ae582a2629. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING189
linux-devel-x86_64WARNING229
source / vignettesOK203
linux-release-x86_64WARNING257
macos-release-arm64WARNING134
macos-oldrel-arm64WARNING236
windows-develWARNING145
windows-releaseWARNING132
windows-oldrelWARNING156
wasm-releaseOK152

Exports:get_ncbi_taxon_idsget_taxon_setsssTaxSEAtaxon_rank_setsTaxSEA

Dependencies:

Single-sample enrichment with ssTaxSEA
Why per-person enrichment? | How it works | Why z-scoring matters | When to use ssTaxSEA vs TaxSEA | Usage | From a count matrix | From a TreeSummarizedExperiment | With custom taxon sets | Interpreting the output | Practical considerations
Rendered fromsingle-sample-enrichment.Rmdusingknitr::rmarkdown

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

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

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: 2025-04-06
Started: 2024-12-09