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)

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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].
Date of publication
None
Maintainer
Andrea Gobbi <gobbi.andrea@mail.com>
License
GPL-3
Version
3.4.0
URLs

View on Bioconductor

Man pages

birewire.analysis.bipartite
Analysis of Jaccard similarity trends across switching steps.
birewire.analysis.dsg
Analysis of Jaccard similarity trends across switching steps.
birewire.analysis.undirected
Analysis of Jaccard similarity trends across switching steps.
birewire.bipartite.from.incidence
Converts an incidence matrix into a bipartite graph.
birewire.build.dsg
Transform a dsg object in a SIF file.
birewire.induced.bipartite
Transform a SIF data frame into a dsg object (a list of...
birewire.load.dsg
Read a SIF file from a given path
BiRewire-package
The BiRewire package
birewire.rewire.bipartite
Efficient rewiring of bipartite graphs
birewire.rewire.bipartite.and.projections
Analysis and rewiring function processing a bipartite graphs...
birewire.rewire.dsg
Efficient rewiring of directed signed graphs
birewire.rewire.undirected
Efficient rewiring of undirected graphs
birewire.sampler.bipartite
Efficient generation of a null model for a given bipartite...
birewire.sampler.dsg
Efficient generation of a null model for a given dsg.
birewire.sampler.undirected
Efficient generation of a null model for a given undirected...
birewire.similarity
Compute the Jaccard similarity index between two binary...
birewire.similarity.dsg
Compute the Jaccard similarity index between dsg.
birewire.slum.to.sparseMatrix
The function transforms a triplet sparse matrix from slum...
birewire.visual.monitoring.bipartite
Visual monitoring of the Markov chain underlying the SA for...
birewire.visual.monitoring.dsg
Visual monitoring of the Markov chain underlying the SA for...
birewire.visual.monitoring.undirected
Visual monitoring of the Markov chain underlying the SA for...
BRCA_binary_matrix
TCGA Brest Cancer data
test_dsg
Tool example of dsg

Files in this package

BiRewire/DESCRIPTION
BiRewire/NAMESPACE
BiRewire/NEWS
BiRewire/R
BiRewire/R/BiRewire.R
BiRewire/build
BiRewire/build/vignette.rds
BiRewire/data
BiRewire/data/BRCA_binary_matrix.RData
BiRewire/data/test_dsg.RData
BiRewire/inst
BiRewire/inst/CITATION
BiRewire/inst/doc
BiRewire/inst/doc/BiRewire.R
BiRewire/inst/doc/BiRewire.Rnw
BiRewire/inst/doc/BiRewire.pdf
BiRewire/inst/unitTests
BiRewire/inst/unitTests/test_allBiRewire.R
BiRewire/man
BiRewire/man/BRCA_binary_matrix.Rd
BiRewire/man/BiRewire-package.Rd
BiRewire/man/birewire.analysis.bipartite.Rd
BiRewire/man/birewire.analysis.dsg.Rd
BiRewire/man/birewire.analysis.undirected.Rd
BiRewire/man/birewire.bipartite.from.incidence.Rd
BiRewire/man/birewire.build.dsg.Rd
BiRewire/man/birewire.induced.bipartite.Rd
BiRewire/man/birewire.load.dsg.Rd
BiRewire/man/birewire.rewire.bipartite.Rd
BiRewire/man/birewire.rewire.bipartite.and.projections.Rd
BiRewire/man/birewire.rewire.dsg.Rd
BiRewire/man/birewire.rewire.undirected.Rd
BiRewire/man/birewire.sampler.bipartite.Rd
BiRewire/man/birewire.sampler.dsg.Rd
BiRewire/man/birewire.sampler.undirected.Rd
BiRewire/man/birewire.similarity.Rd
BiRewire/man/birewire.similarity.dsg.Rd
BiRewire/man/birewire.slum.to.sparseMatrix.Rd
BiRewire/man/birewire.visual.monitoring.bipartite.Rd
BiRewire/man/birewire.visual.monitoring.dsg.Rd
BiRewire/man/birewire.visual.monitoring.undirected.Rd
BiRewire/man/test_dsg.Rd
BiRewire/src
BiRewire/src/BiRewire.c
BiRewire/src/BiRewire.h
BiRewire/src/interface.c
BiRewire/tests
BiRewire/tests/runTests.R
BiRewire/vignettes
BiRewire/vignettes/BiRewire.Rnw
BiRewire/vignettes/analysis.pdf
BiRewire/vignettes/monitoring.pdf