# 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.

- Author
- Andrea Gobbi [aut], Francesco Iorio [aut], Giuseppe Jurman [cbt], Davide Albanese [cbt], Julio Saez-Rodriguez [cbt].
- Date of publication
- None
- Maintainer
- Andrea Gobbi <gobbi.andrea@mail.com>
- License
- GPL-3
- Version
- 3.4.0
- URLs

## 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

## Files in this package

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 |