lefse

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LDA Effect Size (LEfSe) (Segata et. al 2010) is an algorithm for high-dimensional biomarker discovery and explanation that identifies genomic features (genes, pathways, or taxa) characterizing the differences between two or more biological conditions.

Home https://bitbucket.org/nsegata/lefse
Versions 1.0.7, 1.0.7.post1, 1.0.8.post1
License Custom
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/lefse

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install lefse

and update with:

conda update lefse

Notes

Prefix with ‘lefse-‘’ some script names that are rather generic: ‘format_input.py’, ‘plot_cladogram.py’, ‘plot_features.py’, ‘plot_res.py’.

docker

A Docker container is available at https://quay.io/repository/biocontainers/lefse.