To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BiRewire")

In most cases, you don't need to download the package archive at all.

BiRewire

 

   

This is the development version of BiRewire; for the stable release version, see 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: Development (3.5)

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.

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BiRewire")

Documentation

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

browseVignettes("BiRewire")

 

PDF R Script BiRewire
PDF   Reference Manual
Text   NEWS

Details

biocViews Network, Software
Version 3.5.0
In Bioconductor since BioC 2.13 (R-3.0) (3 years)
License GPL-3
Depends igraph, slam, tsne, Matrix
Imports
LinkingTo
Suggests RUnit, BiocGenerics
SystemRequirements
Enhances
URL http://www.ebi.ac.uk/~iorio/BiRewire
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source BiRewire_3.5.0.tar.gz
Windows Binary BiRewire_3.5.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) BiRewire_3.5.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BiRewire
Package Short Url http://bioconductor.org/packages/BiRewire/
Package Downloads Report Download Stats

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