recipe bioconductor-geneplast

Evolutionary and plasticity analysis of orthologous groups

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/geneplast.html

License:

GPL (>= 2)

Recipe:

/bioconductor-geneplast/meta.yaml

Links:

biotools: geneplast, doi: 10.1038/nmeth.3252

Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.

package bioconductor-geneplast

(downloads) docker_bioconductor-geneplast

versions:
1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.3-0,  1.10.0-0,  1.8.0-0,  1.6.2-0,  1.4.0-0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-igraph:

depends r-snow:

requirements:

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 bioconductor-geneplast

and update with::

   mamba update bioconductor-geneplast

To create a new environment, run:

mamba create --name myenvname bioconductor-geneplast

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/bioconductor-geneplast:<tag>

(see `bioconductor-geneplast/tags`_ for valid values for ``<tag>``)

Download stats

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/bioconductor-geneplast/README.html)