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)
Version 3.8.1

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 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].
Bioconductor views Network
Date of publicationNone
MaintainerAndrea Gobbi <gobbi.andrea@mail.com>
LicenseGPL-3
Version3.8.1
URL http://www.ebi.ac.uk/~iorio/BiRewire
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BiRewire")

Getting started

Package overview

Popular man pages

birewire.bipartite.from.incidence: Converts an incidence matrix into a bipartite graph.
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.sampler.undirected: Efficient generation of a null model for a given undirected...
birewire.similarity: Compute the Jaccard similarity index between two binary...
See all...

All man pages Function index File listing

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BiRewire.R
build
build/vignette.rds
data
data/BRCA_binary_matrix.RData
data/test_dsg.RData
inst
inst/CITATION
inst/doc
inst/doc/BiRewire.R
inst/doc/BiRewire.Rnw
inst/doc/BiRewire.pdf
inst/unitTests
inst/unitTests/test_allBiRewire.R
man
man/BRCA_binary_matrix.Rd
man/BiRewire-package.Rd
man/birewire.analysis.bipartite.Rd
man/birewire.analysis.dsg.Rd
man/birewire.analysis.undirected.Rd
man/birewire.bipartite.from.incidence.Rd
man/birewire.build.dsg.Rd
man/birewire.induced.bipartite.Rd
man/birewire.load.dsg.Rd
man/birewire.rewire.bipartite.Rd
man/birewire.rewire.bipartite.and.projections.Rd
man/birewire.rewire.dsg.Rd
man/birewire.rewire.undirected.Rd
man/birewire.sampler.bipartite.Rd
man/birewire.sampler.dsg.Rd
man/birewire.sampler.undirected.Rd
man/birewire.similarity.Rd
man/birewire.similarity.dsg.Rd
man/birewire.slum.to.sparseMatrix.Rd
man/birewire.visual.monitoring.bipartite.Rd
man/birewire.visual.monitoring.dsg.Rd
man/birewire.visual.monitoring.undirected.Rd
man/test_dsg.Rd
src
src/BiRewire.c
src/BiRewire.h
src/interface.c
tests
tests/runTests.R
vignettes
vignettes/BiRewire.Rnw
vignettes/analysis.pdf
vignettes/monitoring.pdf
BiRewire documentation built on May 20, 2017, 10:06 p.m.

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