Overview | Setup and simulation | Running the MCMC sampler | Analyzing the output | Convergence: trace plot | Final sampled network | Recovery of the true network | Posterior summarization by Bayesian model averaging | Visualizing network recovery | Application to real-world biological data | Next steps | Session information
Package: BBNI 0.2.0
BBNI: Bayesian Inference of Boolean Genetic Networks
Implements a fully Bayesian Markov chain Monte Carlo (MCMC) approach for inferring the topology and Boolean logic transition functions of gene regulatory networks from noisy, binary time-series expression data. Network structure and Boolean rules are sampled jointly from their posterior distribution, providing principled uncertainty quantification rather than a single point estimate. Method described in Han et al. (2014) <doi:10.1371/journal.pone.0115806>.
Authors:
BBNI_0.2.0.tar.gz
BBNI_0.2.0.zip(r-4.7)BBNI_0.2.0.zip(r-4.6)BBNI_0.2.0.zip(r-4.5)
BBNI_0.2.0.tgz(r-4.6-any)BBNI_0.2.0.tgz(r-4.5-any)
BBNI_0.2.0.tar.gz(r-4.7-any)BBNI_0.2.0.tar.gz(r-4.6-any)
BBNI_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BBNI/json (API)
| # Install 'BBNI' in R: |
| install.packages('BBNI', repos = c('https://anson-li8.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/anson-li8/bbni/issues
Pkgdown/docs site:https://anson-li8.github.io
Datasets:
- yeast_data - Yeast Cell-Cycle Gene Expression Data
Last updated from:319dcacd5c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 140 | ||
| source / vignettes | OK | 208 | ||
| linux-release-x86_64 | OK | 131 | ||
| macos-release-arm64 | OK | 85 | ||
| macos-oldrel-arm64 | OK | 109 | ||
| windows-devel | OK | 88 | ||
| windows-release | OK | 85 | ||
| windows-oldrel | OK | 74 | ||
| wasm-release | OK | 107 |
Exports:GenerateNetworkGenerateSampleplot_bbniplot_networkplot_tracerun_bbni
Dependencies:bitopsclicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate Initial Network Topology | GenerateNetwork |
| Simulate Boolean Network Observation Dataset | GenerateSample |
| Plot the Inferred Bayesian Boolean Network | plot_bbni |
| Plot a Single Boolean Network | plot_network |
| Plot MCMC Trace for BBNI | plot_trace |
| Execute Metropolis-within-Gibbs MCMC Sampler for Boolean Networks | run_bbni |
| Yeast Cell-Cycle Gene Expression Data | yeast_data |
