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).

Install the latest version of this package by entering the following in R:

```
source("https://bioconductor.org/biocLite.R")
biocLite("BiRewire")
```

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

Bioconductor views | Network |

Date of publication | None |

Maintainer | Andrea Gobbi <gobbi.andrea@mail.com> |

License | GPL-3 |

Version | 3.6.0 |

http://www.ebi.ac.uk/~iorio/BiRewire |

**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

BiRewire | Man page |

birewire.analysis.bipartite | Man page |

birewire.analysis.dsg | Man page |

birewire.analysis.undirected | Man page |

birewire.bipartite.from.incidence | Man page |

birewire.build.dsg | Man page |

birewire.induced.bipartite | Man page |

birewire.load.dsg | Man page |

BiRewire-package | Man page |

birewire.rewire.bipartite | Man page |

birewire.rewire.bipartite.and.projections | Man page |

birewire.rewire.dsg | Man page |

birewire.rewire.undirected | Man page |

birewire.sampler.bipartite | Man page |

birewire.sampler.dsg | Man page |

birewire.sampler.undirected | Man page |

birewire.similarity | Man page |

birewire.similarity.dsg | Man page |

birewire.slum.to.sparseMatrix | Man page |

birewire.visual.monitoring.bipartite | Man page |

birewire.visual.monitoring.dsg | Man page |

birewire.visual.monitoring.undirected | Man page |

BRCA_binary_matrix | Man page |

test_dsg | Man page |

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

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

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