Lefser: Implementation of Metagenomic Biomarker Discovery Tool, LEfSe, in R

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2024 Nov 25

PMID 39585730

Authors

Asya Khleborodova

Samuel D Gamboa-Tuz

Marcel Ramos

Nicola Segata

Levi Waldron

Sehyun Oh

Affiliations

Soon will be listed here.

Abstract

Summary: LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal-Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. We benchmark the performance of lefser against the original algorithm using human and mouse metagenomic datasets.

Availability And Implementation: Our software, lefser, is distributed through the Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/lefser.html), and all the source code is available in the GitHub repository https://github.com/waldronlab/lefser.

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