DOI: 10.18129/B9.bioc.lefser  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see lefser.

R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: 3.16

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] , Levi Waldron [ctb]

Maintainer: Asya Khleborodova <asya.bioconductor at gmail.com>

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


biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License Artistic-2.0
Depends SummarizedExperiment, R (>= 4.0.0)
Imports coin, MASS, ggplot2, stats, methods
Suggests knitr, rmarkdown, curatedMetagenomicData, BiocStyle, testthat, pkgdown, covr, withr
URL https://github.com/waldronlab/lefser
BugReports https://github.com/waldronlab/lefser/issues
Depends On Me
Imports Me ggpicrust2
Suggests Me
Links To Me
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Source Package lefser_1.8.0.tar.gz
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Bioc Package Browser https://code.bioconductor.org/browse/lefser/
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