:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-bionet' .. highlight: bash bioconductor-bionet =================== .. conda:recipe:: bioconductor-bionet :replaces_section_title: :noindex: 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: :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. .. conda:package:: bioconductor-bionet |downloads_bioconductor-bionet| |docker_bioconductor-bionet| :versions: .. raw:: html
1.62.0-01.60.0-01.58.0-01.54.0-01.52.0-01.50.0-11.50.0-01.47.0-01.46.0-0 ``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`` .. raw:: html
: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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-bionet/tags`_ for valid values for ````) .. |downloads_bioconductor-bionet| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-bionet.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-bionet :alt: (downloads) .. |docker_bioconductor-bionet| image:: https://quay.io/repository/biocontainers/bioconductor-bionet/status :target: https://quay.io/repository/biocontainers/bioconductor-bionet .. _`bioconductor-bionet/tags`: https://quay.io/repository/biocontainers/bioconductor-bionet?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-bionet/README.html