<!-- badges: start -->  [](https://codecov.io/gh/waldronlab/lefser?branch=devel) <!-- badges: end --> ## lefser: Run LEfSe in R *lefser* is the R implementation of the Python package, Linear discriminant analysis (LDA) Effect Size ([LEfSe][]). *LEfSe* is the most widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization ([Huttenhower et al. 2011][]). *LEfSe* utilizes standard statistical significance tests along with supplementary tests that incorporate biological consistency and the relevance of effects to identity the features (e.g., organisms, clades, OTU, genes, or functions) that are most likely to account for differences between the two sample groups of interest, referred as ‘classes’. While *LEfSe* is widely used and available in different platform such as Galaxy UI and Conda, there is no convenient way to incorporate it in R-based workflows. Thus, we re-implement *LEfSe* as an R/Bioconductor package, *lefser*. Following the *LEfSe*‘s algorithm including Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis, with some modifications, *lefser* successfully reproduces and improves the original statistical method and the associated plotting functionality. [LEfSe]: https://huttenhower.sph.harvard.edu/galaxy/ [Huttenhower et al. 2011]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218848/