TaxSEA
This is the development version of TaxSEA; for the stable release version, see TaxSEA.
Taxon Set Enrichment Analysis
Bioconductor version: Development (3.22)
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 five previously published databases (BugSigDB, MiMeDB, GutMGene, mBodyMap and GMRepoV2). 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]
Maintainer: Feargal Ryan <feargalr at gmail.com>
citation("TaxSEA")):
Installation
To install this package, start R (version "4.5") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TaxSEA")| TaxSEA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSetEnrichment, Metagenomics, Microbiome, RNASeq, Sequencing, Software |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | stats, utils |
| System Requirements | |
| URL | https://github.com/feargalr/taxsea |
| Bug Reports | https://github.com/feargalr/taxsea/issues |
See More
| Suggests | BiocStyle, bugsigdbr, fgsea, knitr, rmarkdown, 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_1.1.0.tar.gz |
| Windows Binary (x86_64) | TaxSEA_1.1.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |