Package Recipe 'bioconductor-lefser'

recipe bioconductor-lefser

R implementation of the LEfSE method for microbiome biomarker discovery

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/lefser.html
License:: Artistic-2.0
Recipe:: /bioconductor-lefser/meta.yaml

lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).

package bioconductor-lefser¶

Versions:

1.20.2-0, 1.16.0-0, 1.12.1-0, 1.10.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-2, 1.0.0-1

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-ggtree >=4.0.0,<4.1.0
on bioconductor-mia >=1.18.0,<1.19.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-treeio >=1.34.0,<1.35.0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-coin
on r-dplyr
on r-forcats
on r-ggplot2
on r-ggrepel
on r-mass
on r-purrr
on r-stringr
on r-testthat
on r-tibble
on r-tidyr
on r-tidyselect

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-lefser

to add into an existing workspace instead, run:

pixi add bioconductor-lefser

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-lefser

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-lefser

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-lefser:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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/bioconductor-lefser/README.html)