BNrich

0.1.1

Pathway Enrichment Analysis Based on Bayesian Network

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Samaneh MalekniaFirst published 2020-03-202 releasesCRAN page ↗GitHub ↗

Maleknia et al. (2020) doi:10.1101/2020.01.13.905448. A novel pathway enrichment analysis package based on Bayesian network to investigate the topology features of the pathways. firstly, 187 kyoto encyclopedia of genes and genomes (KEGG) human non-metabolic pathways which their cycles were eliminated by biological approach, enter in analysis as Bayesian network structures. The constructed Bayesian network were optimized by the Least Absolute Shrinkage Selector Operator (lasso) and the parameters were learned based on gene expression data. Finally, the impacted pathways were enriched by Fisher’s Exact Test on significant parameters.

Install

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

install.packages("BNrich", 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("Samaneh-Bioinformatics/BNrich")

Development version from Samaneh-Bioinformatics/BNrich. 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-bnrich

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

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-08
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-07
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · staticpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.8K

CRAN downloads in the past year

Rank #13,761 · ~8/day · ~233/mo

Releases R versions

Daily download trend is not available in this view yet.

26330 days

79390 days

2.8K1 year

Compare downloads with other packages →

Also on100 r2u

Repository

GitHub ↗ samaneh-bioinformatics/bnrich

1Stars

0Forks

1Open issues

0Open PRs

0Releases

8Commits

1Contributors

8 commits · Last activity 2020-04-04 · 0% stars, 30d

Stars over time

2026-07-02 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/samaneh-bioinformatics/bnrich on 2026-07-19.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (6)

bnlearn corpcor glmnet graphstatsutils

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Samaneh Maleknia

Author, Maintainer

Authors (2)

Samaneh Maleknia

Author, Maintainer

Mohsen Namazi

Author

Contributors (3)

Kaveh Kavousi

Contributor

Vahid Rezaei-Tabar

Contributor

Ali Sharifi-Zarchi

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.1Latest
2020-04-04 · current release · diff ↗
0.1.0
2020-03-20
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-20
Total releases: 2 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Download size: 872 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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