Package: pastboon 0.1.2
Mohammad Taheri-Ledari
pastboon: Simulation of Parameterized Stochastic Boolean Networks
A Boolean network is a particular kind of discrete dynamical system where the variables are simple binary switches. Despite its simplicity, Boolean network modeling has been a successful method to describe the behavioral pattern of various phenomena. Applying stochastic noise to Boolean networks is a useful approach for representing the effects of various perturbing stimuli on complex systems. A number of methods have been developed to control noise effects on Boolean networks using parameters integrated into the update rules. This package provides functions to examine three such methods: Boolean network with perturbations (BNp), described by Trairatphisan et al. (2013) <doi:10.1186/1478-811X-11-46>, stochastic discrete dynamical systems (SDDS), proposed by Murrugarra et al. (2012) <doi:10.1186/1687-4153-2012-5>, and Boolean network with probabilistic edge weights (PEW), presented by Deritei et al. (2022) <doi:10.1371/journal.pcbi.1010536>. This package includes source code derived from the 'BoolNet' package, which is licensed under the Artistic License 2.0.
Authors:
pastboon_0.1.2.tar.gz
pastboon_0.1.2.tar.gz(r-4.5-noble)pastboon_0.1.2.tar.gz(r-4.4-noble)
pastboon_0.1.2.tgz(r-4.4-emscripten)pastboon_0.1.2.tgz(r-4.3-emscripten)
pastboon.pdf |pastboon.html✨
pastboon/json (API)
| # Install 'pastboon' in R: |
| install.packages('pastboon', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/taherimo/pastboon/issues
- lac_operon_net - The lactose operon Boolean network
Last updated 16 days agofrom:5a80385455. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 23 2024 |
| R-4.5-linux-x86_64 | OK | Aug 23 2024 |
Exports:calc_convergence_timecalc_node_activitiescount_pairwise_transextract_edgesget_reached_states
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulation of Parameterized Stochastic Boolean Networks | pastboon-package pastboon |
| Calculate convergence time-step for node activities | calc_convergence_time |
| Calculate activity rate for each node | calc_node_activities |
| Count pairwise transitions between a given set of states | count_pairwise_trans |
| Extract edges from a Boolean network | extract_edges |
| Obtain the reached states | get_reached_states |
| The lactose operon Boolean network | lac_operon_net |
