lefser

R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: 3.23 · Package version: 1.22.0

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).

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("lefser")

Details

Maintainer	Sehyun Oh <shbrief@gmail.com>
Author	Sehyun Oh [cre, ctb] (ORCID: <https://orcid.org/0000-0002-9490-3061>), Asya Khleborodova [aut], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Ludwig Geistlinger [ctb] (ORCID: <https://orcid.org/0000-0002-2495-5464>), Levi Waldron [ctb] (ORCID: <https://orcid.org/0000-0003-2725-0694>), NCI [fnd] (GrantNo.: R01CA230551)
License	Artistic-2.0
URL	https://github.com/waldronlab/lefser
Bug Reports	https://github.com/waldronlab/lefser/issues
Downloads rank	814
Source branch	RELEASE_3_23
biocViews	Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod

Documentation

lefser: a metagenomic biomarker discovery tool

Download

Source package

Dependencies

Depends: SummarizedExperiment, R (>= 4.5.0)

Imports: coin, MASS, ggplot2 (>= 3.4.0), S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree, BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio

Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, pkgdown, covr, withr

Reverse dependencies

Suggests Me (4): curatedMetagenomicData, dar, ggpicrust2, MiscMetabar