DOI: 10.18129/B9.bioc.bnem  

This is the development version of bnem; for the stable release version, see bnem.

Training of logical models from indirect measurements of perturbation experiments

Bioconductor version: Development (3.18)

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).

Author: Martin Pirkl [aut, cre]

Maintainer: Martin Pirkl <martinpirkl at>

Citation (from within R, enter citation("bnem")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


PDF   Reference Manual


biocViews GeneExpression, GeneRegulation, Network, NetworkInference, Pathways, Preprocessing, Software, SystemsBiology
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
Suggests knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64) bnem_1.9.0.tgz
macOS Binary (arm64) bnem_1.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: