BiRewire
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see 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)
Bioconductor version: 3.16
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.
Author: Andrea Gobbi [aut], Francesco Iorio [aut], Giuseppe Jurman [cbt], Davide Albanese [cbt], Julio Saez-Rodriguez [cbt].
Maintainer: Andrea Gobbi <gobbi.andrea at mail.com>
citation("BiRewire")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiRewire")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BiRewire")| BiRewire | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Network, Software |
| Version | 3.30.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-3 |
| Depends | igraph, slam, Rtsne, Matrix |
| Imports | |
| System Requirements | |
| URL | http://www.ebi.ac.uk/~iorio/BiRewire |
See More
| Suggests | RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiRewire_3.30.0.tar.gz |
| Windows Binary | BiRewire_3.30.0.zip (64-bit only) |
| macOS Binary (x86_64) | BiRewire_3.30.0.tgz |
| macOS Binary (arm64) | BiRewire_3.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiRewire |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiRewire |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiRewire/ |
| Package Short Url | https://bioconductor.org/packages/BiRewire/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |