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BiRewire (version 3.2.1)

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)

Description

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.

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Version

Version

3.2.1

License

GPL-3

Maintainer

Andrea Gobbi

Last Published

February 15th, 2017

Functions in BiRewire (3.2.1)

birewire.build.dsg

Transform a dsg object in a SIF file.
birewire.analysis.undirected

Analysis of Jaccard similarity trends across switching steps.
BRCA_binary_matrix

TCGA Brest Cancer data
birewire.rewire.bipartite

Efficient rewiring of bipartite graphs
birewire.visual.monitoring.dsg

Visual monitoring of the Markov chain underlying the SA for dsgs.
birewire.slum.to.sparseMatrix

The function transforms a triplet sparse matrix from slum package to a Matrix sparse matrix.
birewire.bipartite.from.incidence

Converts an incidence matrix into a bipartite graph.
birewire.sampler.bipartite

Efficient generation of a null model for a given bipartite graph
birewire.sampler.dsg

Efficient generation of a null model for a given dsg.
birewire.rewire.dsg

Efficient rewiring of directed signed graphs
birewire.induced.bipartite

Transform a SIF data frame into a dsg object (a list of positive and negative incidence matrix).
birewire.load.dsg

Read a SIF file from a given path
birewire.similarity

Compute the Jaccard similarity index between two binary matrices with the same number of non-null entries and the sam row- and column-wise sums.
BiRewire-package

The BiRewire package
birewire.analysis.bipartite

Analysis of Jaccard similarity trends across switching steps.
birewire.rewire.bipartite.and.projections

Analysis and rewiring function processing a bipartite graphs and its two projections
birewire.sampler.undirected

Efficient generation of a null model for a given undirected graph
test_dsg

Tool example of dsg
birewire.visual.monitoring.undirected

Visual monitoring of the Markov chain underlying the SA for undirected graphs.
birewire.visual.monitoring.bipartite

Visual monitoring of the Markov chain underlying the SA for directed graphs.
birewire.analysis.dsg

Analysis of Jaccard similarity trends across switching steps.
birewire.rewire.undirected

Efficient rewiring of undirected graphs
birewire.similarity.dsg

Compute the Jaccard similarity index between dsg.