TaxSEA
Bioc currentTaxon Set Enrichment Analysis
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 5 exported
Complexity
9.2 avg / 23 max
Call network
13 nodes / 12 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,697
Files
40
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
7
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-04-15
Latest release
2026-04-28
Avg cadence
189 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 8
- Examples that run
- 88%7 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
5 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/feargalr/taxsea on 2026-10-22.
The R CMD check workflow runs on Linux, and on R-devel
GitHub Pages site last deployed 2026-09-21 · The repository has a site deploy workflow
pkgdown site last built 2026-09-21
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| NCBI_ids | list | 12,772 elements | No other package |
| TaxSEA_db | list | 651 elements | No other package |
| TaxSEA_test_data | vector | 164 elements | No other package |
Topics
People
-
Feargal Ryan
author
maintainer
funder
Supported by NHMRC Investigator Grant
Cite
Cite this package
Run in R for the authors' entry:
citation("TaxSEA")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bib/bbaf173.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.