lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R

• Published in: Bioinformatics (Oxford, England) Vol. 40; no. 12
• Main Authors: Khleborodova, Asya, Gamboa-Tuz, Samuel D, Ramos, Marcel, Segata, Nicola, Waldron, Levi, Oh, Sehyun
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 28.11.2024; Oxford Publishing Limited (England)
• Subjects: Algorithms; Animals; Applications Note; Availability; Biomarkers; Data analysis; Discriminant analysis; Humans; HyperText Markup Language; Metagenomics; Metagenomics - methods; Mice; Software; Source code; Statistical analysis
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btae707

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.