Package: BiRewire 3.37.0

Andrea Gobbi

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). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.

Authors:Andrea Gobbi [aut], Francesco Iorio [aut], Giuseppe Jurman [cbt], Davide Albanese [cbt], Julio Saez-Rodriguez [cbt].

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NEWS

# Install 'BiRewire' in R:
install.packages('BiRewire', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:BiRewire-3.37.0(bioc 3.20)BiRewire-3.36.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

20 exports 2.05 score 14 dependencies 5 mentions

Last updated 2 months agofrom:5f4185dcdc

Exports:birewire.analysis.bipartitebirewire.analysis.dsgbirewire.analysis.undirectedbirewire.bipartite.from.incidencebirewire.build.dsgbirewire.induced.bipartitebirewire.load.dsgbirewire.rewire.bipartitebirewire.rewire.bipartite.and.projectionsbirewire.rewire.dsgbirewire.rewire.undirectedbirewire.sampler.bipartitebirewire.sampler.dsgbirewire.sampler.undirectedbirewire.similaritybirewire.similarity.dsgbirewire.slum.to.sparseMatrixbirewire.visual.monitoring.bipartitebirewire.visual.monitoring.dsgbirewire.visual.monitoring.undirected

Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigRcpprlangRtsneslamvctrs

BiRewire

Rendered fromBiRewire.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2022-03-28
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
The BiRewire packageBiRewire-package BiRewire
Analysis of Jaccard similarity trends across switching steps.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
Converts an incidence matrix into a bipartite graph.birewire.bipartite.from.incidence
Transform a dsg object in a SIF file.birewire.build.dsg
Transform a SIF data frame into a dsg object (a list of positive and negative incidence matrix).birewire.induced.bipartite
Read a SIF file from a given pathbirewire.load.dsg
Efficient rewiring of bipartite graphsbirewire.rewire.bipartite
Analysis and rewiring function processing a bipartite graphs and its two projectionsbirewire.rewire.bipartite.and.projections
Efficient rewiring of directed signed graphsbirewire.rewire.dsg
Efficient rewiring of undirected graphsbirewire.rewire.undirected
Efficient generation of a null model for a given bipartite graphbirewire.sampler.bipartite
Efficient generation of a null model for a given dsg.birewire.sampler.dsg
Efficient generation of a null model for a given undirected graphbirewire.sampler.undirected
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.similarity
Compute the Jaccard similarity index between dsg.birewire.similarity.dsg
The function transforms a triplet sparse matrix from slum package to a Matrix sparse matrix.birewire.slum.to.sparseMatrix
Visual monitoring of the Markov chain underlying the SA for directed graphs.birewire.visual.monitoring.bipartite
Visual monitoring of the Markov chain underlying the SA for dsgs.birewire.visual.monitoring.dsg
Visual monitoring of the Markov chain underlying the SA for undirected graphs.birewire.visual.monitoring.undirected
TCGA Brest Cancer dataBRCA_binary_matrix
Tool example of dsgtest_dsg