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R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: Release (3.19)

lefser is an implementation in R of the popular "LDA Effect Size (LEfSe)" method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.

Author: Asya Khleborodova [cre, aut], Ludwig Geistlinger [ctb], Marcel Ramos [ctb] , Samuel Gamboa-Tuz [ctb], Levi Waldron [ctb], Sehyun Oh [ctb]

Maintainer: Asya Khleborodova <asya.bioconductor at>

Citation (from within R, enter citation("lefser")):


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Introduction to the lefser R implementation of the popular LEfSE software for biomarker discovery in microbiome analysis. HTML R Script
Reference Manual PDF


biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends SummarizedExperiment, R (>= 4.0.0)
Imports coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr
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Suggests knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr
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Source Package lefser_1.14.0.tar.gz
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