# 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)

## Documentation for package ‘BiRewire’ version 3.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BiRewire-package | The BiRewire package
BiRewire | The BiRewire package
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 positive and negative incidence matrix).
birewire.load.dsg | Read a SIF file from a given path
birewire.rewire.bipartite | Efficient rewiring of bipartite graphs
birewire.rewire.bipartite.and.projections | Analysis and rewiring function processing a bipartite graphs and its two projections
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 graph
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 graph
birewire.similarity | 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.dsg | Compute the Jaccard similarity index between dsg.
birewire.slum.to.sparseMatrix | The function transforms a triplet sparse matrix from slum package to a Matrix sparse matrix.
birewire.visual.monitoring.bipartite | Visual monitoring of the Markov chain underlying the SA for directed graphs.
birewire.visual.monitoring.dsg | Visual monitoring of the Markov chain underlying the SA for dsgs.
birewire.visual.monitoring.undirected | Visual monitoring of the Markov chain underlying the SA for undirected graphs.
BRCA_binary_matrix | TCGA Brest Cancer data
test_dsg | Tool example of dsg