:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'lefse' .. highlight: bash lefse ===== .. conda:recipe:: lefse :replaces_section_title: :noindex: 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. :homepage: https://github.com/SegataLab/lefse :license: MIT :recipe: /`lefse `_/`meta.yaml `_ .. conda:package:: lefse |downloads_lefse| |docker_lefse| :versions: ``1.1.2-0``,  ``1.1.1-0``,  ``1.0.8.post1-2``,  ``1.0.8.post1-1``,  ``1.0.8.post1-0``,  ``1.0.7.post1-0``,  ``1.0.7-2``,  ``1.0.7-1`` :depends biom-format: :depends icu: :depends matplotlib-base: :depends numpy: :depends python: ``>=3.7`` :depends r-base: :depends r-coin: :depends r-mass: :depends r-modeltools: :depends r-mvtnorm: :depends r-survival: :depends rpy2: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 lefse and update with:: mamba update lefse To create a new environment, run:: mamba create --name myenvname lefse 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 quay.io/biocontainers/lefse: (see `lefse/tags`_ for valid values for ````) .. |downloads_lefse| image:: https://img.shields.io/conda/dn/bioconda/lefse.svg?style=flat :target: https://anaconda.org/bioconda/lefse :alt: (downloads) .. |docker_lefse| image:: https://quay.io/repository/biocontainers/lefse/status :target: https://quay.io/repository/biocontainers/lefse .. _`lefse/tags`: https://quay.io/repository/biocontainers/lefse?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/lefse/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/lefse/README.html