BoolNet is an R package for generation, reconstruction, simulation and analysis of synchronous, asynchronous and probabilistic Boolean networks. This page provides help on the installation and usage of the package. The most recent version of the package and its documentation is available from BoolNet's CRAN page.
Documentation is included in the R package. You can get help for a command by typing ?<command> (e.g. ?getAttractors) inside R when the package is loaded.
Additionally, a step-by-step tutorial is available here.
The most recent source and binary packages for BoolNet are available from CRAN. The Debian Med team also maintains a package r-cran-boolnet which can be obtained from the official repositories for Debian and Ubuntu.
In an R console, type install.packages("BoolNet"). The package is now installed and can be loaded via library(BoolNet). The packages igraph and XML are installed automatically, as BoolNet depends on them.
To install BoolNet from the official Debian/Ubuntu repositories, open a terminal and type
sudo apt-get install r-cran-boolnet
Please note that the Debian package may not always be the most recent version of BoolNet.
To install BoolNet manually, the sources (BoolNet_<version>.tar.gz) must be downloaded from CRAN and compiled. As a prerequisite, the packages igraph and XML must be installed.
To cite the package in publications, use:
C. Müssel, M. Hopfensitz, and H. A. Kestler. BoolNet - an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics, 26(10):1378–1380, 2010.
Our paper "A model of the onset of the Senescence Associated Secretory Phenotype after DNA damage induced Senescence" has been accepted for publishing in PLOS Computational Biology.
Our paper "The influence of multi-class feature selection on the prediction of diagnostic phenotypes" has been accepted for publishing in Neural Processing Letters.