networkABC: Network Reverse Engineering with Approximate Bayesian Computation

We developed an inference tool based on approximate Bayesian computation to decipher network data and assess the strength of the inferred links between network's actors. It is a new multi-level approximate Bayesian computation (ABC) approach. At the first level, the method captures the global properties of the network, such as a scale-free structure and clustering coefficients, whereas the second level is targeted to capture local properties, including the probability of each couple of genes being linked. Up to now, Approximate Bayesian Computation (ABC) algorithms have been scarcely used in that setting and, due to the computational overhead, their application was limited to a small number of genes. On the contrary, our algorithm was made to cope with that issue and has low computational cost. It can be used, for instance, for elucidating gene regulatory network, which is an important step towards understanding the normal cell physiology and complex pathological phenotype. Reverse-engineering consists in using gene expressions over time or over different experimental conditions to discover the structure of the gene network in a targeted cellular process. The fact that gene expression data are usually noisy, highly correlated, and have high dimensionality explains the need for specific statistical methods to reverse engineer the underlying network.

Version: 0.8-1
Depends: R (≥ 3.0.0)
Imports: RColorBrewer, network, sna
Suggests: ggplot2, knitr, markdown, rmarkdown
Published: 2022-10-19
DOI: 10.32614/CRAN.package.networkABC
Author: Frederic Bertrand ORCID iD [cre, aut], Myriam Maumy-Bertrand ORCID iD [aut], Khadija Musayeva [ctb], Nicolas Jung [ctb], Université de Strasbourg [cph], CNRS [cph]
Maintainer: Frederic Bertrand <frederic.bertrand at>
License: GPL-3
NeedsCompilation: yes
Classification/MSC: 62E17, 62F15, 62J07, 62P10, 92C42
Citation: networkABC citation info
Materials: README NEWS
In views: Omics
CRAN checks: networkABC results


Reference manual: networkABC.pdf
Vignettes: Using the networkABC package


Package source: networkABC_0.8-1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): networkABC_0.8-1.tgz, r-oldrel (arm64): networkABC_0.8-1.tgz, r-release (x86_64): networkABC_0.8-1.tgz, r-oldrel (x86_64): networkABC_0.8-1.tgz
Old sources: networkABC archive


Please use the canonical form to link to this page.