recipe bioconductor-lefser

R implementation of the LEfSE method for microbiome biomarker discovery






lefser is an implementation in R of the popular "LDA Effect Size (LEfSe)" method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.

package bioconductor-lefser

(downloads) docker_bioconductor-lefser



depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-coin:

depends r-ggplot2:

depends r-mass:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-lefser

and update with::

   mamba update bioconductor-lefser

To create a new environment, run:

mamba create --name myenvname bioconductor-lefser

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-lefser/tags`_ for valid values for ``<tag>``)

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