BiRewire

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

Bioconductor version: Release (3.17)

Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.

Author: Andrea Gobbi [aut], Francesco Iorio [aut], Giuseppe Jurman [cbt], Davide Albanese [cbt], Julio Saez-Rodriguez [cbt].

Maintainer: Andrea Gobbi <gobbi.andrea at mail.com>

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("BiRewire")

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("BiRewire")

BiRewire	PDF	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Network, Software
Version	3.32.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 years)
License	GPL-3
Depends	igraph, slam, Rtsne, Matrix
Imports
Linking To
Suggests	RUnit, BiocGenerics
System Requirements
Enhances
URL	http://www.ebi.ac.uk/~iorio/BiRewire

Depends On Me
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Package Archives

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

Source Package	BiRewire_3.32.0.tar.gz
Windows Binary	BiRewire_3.32.0.zip (64-bit only)
macOS Binary (x86_64)	BiRewire_3.32.0.tgz
macOS Binary (arm64)	BiRewire_3.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiRewire
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiRewire
Bioc Package Browser	https://code.bioconductor.org/browse/BiRewire/
Package Short Url	https://bioconductor.org/packages/BiRewire/
Package Downloads Report	Download Stats