TaxSEA
This is the development version of TaxSEA; for the stable release version, see TaxSEA.
All Bioconductor versions of TaxSEA
3.24 (devel), 3.23 (release), 3.22, 3.21
Taxon Set Enrichment Analysis
Bioconductor version: 3.24 · Package version: 1.5.7
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.
Author: Feargal Ryan [aut, cre, fnd] (ORCID: 
, funding: Supported by NHMRC Investigator Grant)
Maintainer: Feargal Ryan <feargalr at gmail.com>
Citation
From within R, enter citation("TaxSEA"):
Feargal Ryan. TaxSEA: Taxon Set Enrichment Analysis. doi:10.18129/B9.bioc.TaxSEA, R package version 1.5.7, https://bioconductor.org/packages/TaxSEA.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TaxSEA")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.5.7 |
| License | GPL-3 |
| URL | https://github.com/feargalr/taxsea https://feargalr.github.io/TaxSEA/ |
| Bug Reports | https://github.com/feargalr/taxsea/issues |
| Last updated | 2026-09-21 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2161 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneSetEnrichment, Metagenomics, Microbiome, RNASeq, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/TaxSEA/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TaxSEA")| Analysis types | HTML | |
| Frequently Asked Questions | HTML | |
| Single-sample enrichment with ssTaxSEA | HTML | R Script |
| Testing higher taxonomic levels without collapsing your data | HTML | |
| TaxSEA | HTML | R Script |
| Why use taxon set enrichment analysis? | HTML | |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | TaxSEA_1.5.7.tar.gz |
| Windows binary (x86_64) | TaxSEA_1.5.7.zip |
| macOS binary (arm64) | TaxSEA_1.5.7.tgz |
| macOS binary (x86_64) | TaxSEA_1.5.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TaxSEA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TaxSEA |
| Package Downloads Report | Download Stats |