BBNI

0.1.1

Bayesian Inference of Boolean Genetic Networks

0packages depend

120downloads / year

6.5%test coverage

12/13checks pass

Overview

About

Maintained by Anson LiFirst published 2026-07-151 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("BBNI", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("anson-li8/BBNI")

Development version from anson-li8/BBNI. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bbni

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-BBNI

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.1 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.03

6.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-16
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 215 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

120

CRAN downloads in the past year

Rank #24,518 · ~0/day · ~10/mo

Releases R versions

Daily download trend is not available in this view yet.

12030 days

12090 days

1201 year

Compare downloads with other packages →

Also on9 r2u1 autocran

Repository

GitHub ↗ anson-li8/bbni

0Stars

0Forks

0Open issues

0Open PRs

5Releases

125Commits

1Contributors

bayesian-inferencebinary-networkgene-expressionnoisy-datar-package

125 commits · Last activity 2026-07-22

Releases over time

2026-07-16 · 22026-07-23 · 5

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/anson-li8/bbni on 2026-08-03.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (2)

lintrRStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (2)

bitopsstats

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Anson Li

Author, Maintainer

Authors (2)

Anson Li

Author, Maintainer

Shengtong Han

Author

Package Timeline

1 release. R releases are shown for context.

0.1.1Latest
2026-07-15 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-15
Total releases: 1 / 1 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →