recipe lefse

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

package lefse

(downloads) 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:

additional platforms:

Installation

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 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:<tag>

(see `lefse/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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