This is the development version of lefser; for the stable release version, see lefser.
R implementation of the LEfSE method for microbiome biomarker discoveryBioconductor version: Development (3.22)
lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).
Author: Sehyun Oh [cre, ctb] ORCID: 0000-0002-9490-3061 , Asya Khleborodova [aut], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb] ORCID: 0000-0002-3242-0582 , Ludwig Geistlinger [ctb] ORCID: 0000-0002-2495-5464 , Levi Waldron [ctb] ORCID: 0000-0003-2725-0694
Maintainer: Sehyun Oh <shbrief at gmail.com>
Citation (from within R, entercitation("lefser")
): 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("lefser")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("lefser")
Details biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod Version 1.19.1 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License Artistic-2.0 Depends SummarizedExperiment, R (>= 4.5.0) Imports coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree, BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio System Requirements URL https://github.com/waldronlab/lefser Bug Reports https://github.com/waldronlab/lefser/issues See More Package Archives
Follow Installation instructions to use this package in your R session.
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