Related Experiment Video
Updated: Jun 6, 2025
Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size LEfSe in Microbiome Data
Published on: May 16, 2022
lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R
Asya Khleborodova1,2, Samuel D Gamboa-Tuz1,2, Marcel Ramos1,2
1Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY 10027, United States.
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.
