recipe bioconductor-gnet2

Constructing gene regulatory networks from expression data through functional module inference

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/GNET2.html

License:

Apache License 2.0

Recipe:

/bioconductor-gnet2/meta.yaml

Links:

biotools: gnet2

Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.

package bioconductor-gnet2

versions:

1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-diagrammer:

depends r-dplyr:

depends r-ggplot2:

depends r-igraph:

depends r-matrixstats:

depends r-rcpp:

depends r-reshape2:

depends r-xgboost:

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-gnet2

and update with::

   mamba update bioconductor-gnet2

To create a new environment, run:

mamba create --name myenvname bioconductor-gnet2

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-gnet2:<tag>

(see `bioconductor-gnet2/tags`_ for valid values for ``<tag>``)

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