TaxSEA
This is the development version of TaxSEA; for the stable release version, see TaxSEA.
Taxon Set Enrichment Analysis
Bioconductor version: Development (3.24)
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.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | R Script |
| 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 | 1.5.7 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.6.0) |
| Imports | methods, 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, S4Vectors, 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_1.5.7.tar.gz |
| Windows Binary (x86_64) | TaxSEA_1.5.5.zip |
| macOS Binary (big-sur-x86_64) | TaxSEA_1.5.7.tgz |
| macOS Binary (sonoma-arm64) | TaxSEA_1.5.7.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 |