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://bitbucket.org/nsegata/lefse

License

Custom

Recipe

/lefse/meta.yaml

package lefse

(downloads) docker_lefse

Versions

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

>=2.1.5

Depends icu

58.*

Depends matplotlib

>=1.0,<2.2.0

Depends numpy

Depends python

<3

Depends r-base

Depends r-coin

Depends r-mass

Depends r-modeltools

Depends r-mvtnorm

Depends r-survival

Depends rpy2

>=2.8.5

Requirements

Installation

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

conda install lefse

and update with:

conda update lefse

or use the docker container:

docker pull quay.io/biocontainers/lefse:<tag>

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

Notes

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

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)