Maximal Biclique Enumeration in Bipartite Graphs

https://cran.r-project.org/package=biclique

Description

A tool for enumerating maximal complete bipartite graphs. The input file should be tab delimited. This package supports edgelist and binary matrix format. You can try the example files in the inst directory. The output are maximal complete bipartite graphs.

Installation

The stable, CRAN-ready version can be installed with:

install.packages("biclique")

The latest version can be obtained via:

devtools::install_github("YupingLu/biclique")

Examples

Load the package

library(biclique)

Add the number of vertices and edges to the original input graph. If your input file already has these values, you don't have to run this command.

bi.format("example2.el")       #edgelist format
bi.format("example5.bmat", 1)  #binary matrix format

Input: edgelist format.

degreelist = bi.degree("example1.el")  #Compute the degree of each vertex
bicliques = bi.clique("example1.el")   #Compute the bicliques
bi.print()                             #Print the bicliques

You can also choose the threshold size for computed bicliques.

bicliques = bi.clique("example1.el", 3, 2)  #bicliques larger or equal to K3,2

Input: binary matrix format.

degreelist = bi.degree("example4.bmat", filetype = 1)  #Compute the degree of each vertex
bicliques = bi.clique("example4.bmat", filetype = 1)   #Compute the bicliques
bi.print()                                             #Print the bicliques

For more details, please check the documentation.

Ask Questions

Please use biclique/issues for how to use biclique and reporting bugs

License

Reference Paper

Lu, Y., Phillips, C.A. & Langston, M.A. Biclique: an R package for maximal biclique enumeration in bipartite graphs. BMC Res Notes 13, 88 (2020). https://doi.org/10.1186/s13104-020-04955-0

YupingLu / biclique

readme