recipe bioconductor-bionet

Routines for the functional analysis of biological networks

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-bionet/meta.yaml

Links:

biotools: bionet

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.

package bioconductor-bionet

(downloads) docker_bioconductor-bionet

versions:
1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.47.0-0,  1.46.0-0, 

1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.47.0-0,  1.46.0-0,  1.44.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-rbgl:

>=1.78.0,<1.79.0

depends r-base:

>=4.3,<4.4.0a0

depends r-igraph:

>=1.0.1

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-bionet

and update with::

   mamba update bioconductor-bionet

To create a new environment, run:

mamba create --name myenvname bioconductor-bionet

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-bionet:<tag>

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

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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-bionet/README.html)