BioNet

This is the released version of BioNet; for the devel version, see BioNet.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7

Routines for the functional analysis of biological networks

Bioconductor version: Release (3.23)

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.

Author: Marcus Dittrich and Daniela Beisser

Maintainer: Marcus Dittrich <marcus.dittrich at biozentrum.uni-wuerzburg.de>

Citation (from within R, enter citation("BioNet")):

Marcus Dittrich and Daniela Beisser. BioNet: Routines for the functional analysis of biological networks. doi:10.18129/B9.bioc.BioNet, R package version 1.72.0, https://bioconductor.org/packages/BioNet.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BioNet")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BioNet")

BioNet Tutorial	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software
Version	1.72.0
In Bioconductor since	BioC 2.7 (R-2.12) (16 years)
License	GPL (>= 2)
Depends	R (>= 2.10.0), graph, RBGL
Imports	igraph (>= 1.0.1), AnnotationDbi, Biobase
System Requirements
URL	http://bionet.bioapps.biozentrum.uni-wuerzburg.de/

Suggests	rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML
Linking To
Enhances
Depends On Me
Imports Me	gatom, SMITE
Suggests Me	mwcsr, SANTA
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BioNet_1.72.0.tar.gz
Windows Binary (x86_64)	BioNet_1.72.0.zip
macOS Binary (big-sur-x86_64)	BioNet_1.72.0.tgz
macOS Binary (sonoma-arm64)	BioNet_1.72.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BioNet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BioNet
Package Short Url	https://bioconductor.org/packages/BioNet/
Package Downloads Report	Download Stats