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This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see BiRewire.

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

Bioconductor version: 3.1

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 function for the analysis of the introduced randomness across the switching and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks (not bipartite) 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 useful and a visual montioring of the underlying Markov Chain has been implemented.

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

Maintainer: Andrea Gobbi <gobbi.andrea at>

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PDF R Script BiRewire
PDF   Reference Manual


biocViews Network, Software
Version 2.2.3
In Bioconductor since BioC 2.13 (R-3.0) (2.5 years)
License GPL-3
Depends igraph, slam, tsne
Suggests RUnit, BiocGenerics
Depends On Me
Imports Me
Suggests Me
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