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).
Author  Andrea Gobbi [aut], Francesco Iorio [aut], Giuseppe Jurman [cbt], Davide Albanese [cbt], Julio SaezRodriguez [cbt]. 
Bioconductor views  Network 
Date of publication  None 
Maintainer  Andrea Gobbi <gobbi.andrea@mail.com> 
License  GPL3 
Version  3.8.1 
URL  http://www.ebi.ac.uk/~iorio/BiRewire 
Package repository  View on Bioconductor 
Installation  Install the latest version of this package by entering the following in R:



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  
BiRewirepackage: 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/BiRewirepackage.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

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