networkABC

0.9-1

Network Reverse Engineering with Approximate Bayesian Computation

0packages depend

3.2Kdownloads / year

68.7%test coverage

13/13checks pass

Overview

About

Maintained by Frederic BertrandFirst published 2019-03-067 releasesCRAN page ↗GitHub ↗

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.

Install

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

install.packages("networkABC", 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("fbertran/networkABC")

Development version from fbertran/networkABC. 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-networkabc

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-networkABC

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

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.52

68.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 414 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 43%
References docs: 20%

Downloads

3.2K

CRAN downloads in the past year

Rank #14,019 · ~9/day · ~265/mo

Releases R versions

Daily download trend is not available in this view yet.

23330 days

75190 days

3.2K1 year

Compare downloads with other packages →

Also on441 r2u28 autocran23 c2d4u

Repository

GitHub ↗ fbertran/networkabc

4Stars

1Forks

0Open issues

0Open PRs

3Releases

38Commits

1Contributors

38 commits · Last activity 2025-09-19

Stars over time

2024-06-05 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fbertran/networkabc on 2026-07-26.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (3)

RColorBrewer network sna

LinkingTo (0)

none

Suggests (5)

ggplot2 knitr markdown rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Frederic Bertrand

Maintainer, Author

Authors (2)

Frederic Bertrand

Maintainer, Author

Myriam Maumy-Bertrand

Author

Contributors (2)

Nicolas Jung

Contributor

Khadija Musayeva

Contributor

CNRS

Université de Strasbourg

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.9-1Latest
2025-09-20 · current release · diff ↗
0.9-0
2025-08-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.8-1
2022-10-19 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.8-0
2021-03-20 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.7-0
2020-03-03 · diff ↗
0.6-0
2020-02-07 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.5-3
2019-03-06
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-06
Total releases: 7 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 8.3 KB / 3 files
Download size: 352 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Report a problem with this page →