TaxSEA

This is the development version of TaxSEA; for the stable release version, see TaxSEA.

Taxon Set Enrichment Analysis

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DOI: 10.18129/B9.bioc.TaxSEA

Bioconductor version: Development (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] ORCID iD ORCID: 0000-0002-1565-4598

Maintainer: Feargal Ryan <feargalr at gmail.com>

Citation (from within R, enter citation("TaxSEA")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("TaxSEA")

For older versions of R, please refer to the appropriate Bioconductor release.