recipe bioconductor-bionet

Routines for the functional analysis of biological networks

Homepage

https://bioconductor.org/packages/3.10/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

Versions

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 >=1.48.0,<1.49.0

• bioconductor-biobase >=2.46.0,<2.47.0

• bioconductor-graph >=1.64.0,<1.65.0

• bioconductor-rbgl >=1.62.0,<1.63.0

• r-base >=3.6,<3.7.0a0

• r-igraph >=1.0.1

Required By

• bioconductor-htsanalyzer

• bioconductor-smite

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-bionet

and update with:

conda update bioconductor-bionet

or use the docker container:

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

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

Link to this page

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