Installation

The current version is ebdbNet version 1.1. It may be downloaded below:

It may also be downloaded from CRAN. In addition, if your computer has an internet connection, you may install the ebdbNet package by typing install.packages("ebdbNet") at the R prompt.

ebdbNet requires a recent version of R (at least version 2.8.1). The current version 1.1 of ebdbNet suggests prior installation of the packages GeneNet and Rgraphviz, although these are not required for ebdbNet to work. GeneNet is suggested as it contains several example datasets, and contains methods which may be easily compared to the EBDBN method in ebdbNet. Rgraphviz is suggested as it enables visualization of networks within R.

Network visualization

To visualize networks inferred by ebdbNet, we suggest one of two options:

  • Cytoscape, an open source bioinformatics software platform
  • Rgraphviz, a Bioconductor package

To visualize networks, the user can invoke the function visualize in ebdbNet to put results in the appropriate format. For Rgraphviz, the user must install the graph visualization software graphviz in addition to Rgraphviz. See the README file in the source distribution of Rgraphviz for more details (particularly for Windows users, who may experience some difficulties during installation).

ebdbNet: Previous releases

Previous releases of ebdbNet may also be downloaded below, although these are obsolete and should only be used for reference: