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)

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).

AuthorAndrea Gobbi [aut], Francesco Iorio [aut], Giuseppe Jurman [cbt], Davide Albanese [cbt], Julio Saez-Rodriguez [cbt].
Date of publicationNone
MaintainerAndrea Gobbi <gobbi.andrea@mail.com>
LicenseGPL-3
Version3.6.0
http://www.ebi.ac.uk/~iorio/BiRewire

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

Functions

BiRewire Man page
birewire.analysis.bipartite Man page
birewire.analysis.dsg Man page
birewire.analysis.undirected Man page
birewire.bipartite.from.incidence Man page
birewire.build.dsg Man page
birewire.induced.bipartite Man page
birewire.load.dsg Man page
BiRewire-package Man page
birewire.rewire.bipartite Man page
birewire.rewire.bipartite.and.projections Man page
birewire.rewire.dsg Man page
birewire.rewire.undirected Man page
birewire.sampler.bipartite Man page
birewire.sampler.dsg Man page
birewire.sampler.undirected Man page
birewire.similarity Man page
birewire.similarity.dsg Man page
birewire.slum.to.sparseMatrix Man page
birewire.visual.monitoring.bipartite Man page
birewire.visual.monitoring.dsg Man page
birewire.visual.monitoring.undirected Man page
BRCA_binary_matrix Man page
test_dsg Man page

Files

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

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