Name Mode Size
.github 040000
R 040000
data 040000
inst 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
DESCRIPTION 100644 1 kb
NAMESPACE 100644 1 kb 100644 0 kb 100644 1 kb
_pkgdown.yml 100644 0 kb
codecov.yml 100644 0 kb
<!-- badges: start --> ![build]( [![Codecov test coverage](]( <!-- badges: end --> # lefser: Run LEfSE in R `lefser` is the R implementation of the _LEfSe_ method for microbiome biomarker discovery[1]. The original software is likely the most widely-used method for biomarker discovery and plotting in microbiome studies, with ~5,000 citations as of the end of 2020. However, the original software is implemented in Python as a command-line tool and Galaxy module, and is not straightforward to implement in R. The method involves Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers in groups and sub-group blocks. `lefser` closely reproduces the original statistical method and the associated barplot of results. [1] Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C: Metagenomic biomarker discovery and explanation. Genome Biol. 2011, 12:R60.