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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| analysis_types | HTML | |
| frequently asked questions | 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/TaxSEA/ |
| Package Short Url | https://bioconductor.org/packages/TaxSEA/ |
| Package Downloads Report | Download Stats |