TaxSEA
Taxon Set Enrichment Analysis
Bioconductor version: 3.24 · Package version: 1.5.7
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TaxSEA")Details
| Maintainer | Feargal Ryan <feargalr@gmail.com> |
| Author | Feargal Ryan [aut, cre, fnd] (ORCID: <https://orcid.org/0000-0002-1565-4598>, funding: Supported by NHMRC Investigator Grant) |
| License | GPL-3 |
| URL | https://github.com/feargalr/taxsea, https://feargalr.github.io/TaxSEA/ |
| Bug Reports | https://github.com/feargalr/taxsea/issues |
| 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/ |
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.
Documentation
- Analysis types
- Frequently Asked Questions
- Single-sample enrichment with ssTaxSEA
- Testing higher taxonomic levels without collapsing your data
- TaxSEA
- Why use taxon set enrichment analysis?
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 |