TaxSEA
This is the released version of TaxSEA; for the devel version, see TaxSEA.
Taxon Set Enrichment Analysis
Bioconductor version: Release (3.23)
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.
Author: Feargal Ryan [aut, cre, fnd] (ORCID: 
, funding: Supported by NHMRC Investigator Grant)
Maintainer: Feargal Ryan <feargalr at gmail.com>
citation("TaxSEA")):Feargal Ryan. TaxSEA: Taxon Set Enrichment Analysis. doi:10.18129/B9.bioc.TaxSEA, R package version 1.4.0, 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")
BiocManager::install("TaxSEA")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TaxSEA")| frequently asked questions | HTML | |
| analysis_types | HTML | |
| single_sample_enrichment | HTML | |
| taxonomic_aggregation | HTML | |
| TaxSEA | HTML | R Script |
| Why use taxon set enrichment analysis? | HTML | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSetEnrichment, Metagenomics, Microbiome, RNASeq, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | stats, utils |
| System Requirements | |
| URL | https://github.com/feargalr/taxsea https://feargalr.github.io/TaxSEA/ |
| Bug Reports | https://github.com/feargalr/taxsea/issues |
See More
| Suggests | BiocStyle, bugsigdbr, fgsea, knitr, mia, rmarkdown, SummarizedExperiment, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TaxSEA_1.4.0.tar.gz |
| Windows Binary (x86_64) | TaxSEA_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | TaxSEA_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | TaxSEA_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TaxSEA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TaxSEA |
| Package Short Url | https://bioconductor.org/packages/TaxSEA/ |
| Package Downloads Report | Download Stats |