Welcome to the new bioconductor.org!

bnem

Training of logical models from indirect measurements of perturbation experiments


Bioconductor version: Release (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 yahoo.de>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("bnem")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bnem")
bnem.html HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneRegulation, Network, NetworkInference, Pathways, Preprocessing, Software, SystemsBiology
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
System Requirements
URL https://github.com/MartinFXP/bnem/
Bug Reports https://github.com/MartinFXP/bnem/issues
See More
Suggests knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package bnem_1.10.0.tar.gz
Windows Binary bnem_1.10.0.zip (64-bit only)
macOS Binary (x86_64) bnem_1.10.0.tgz
macOS Binary (arm64) bnem_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bnem
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bnem
Bioc Package Browser https://code.bioconductor.org/browse/bnem/
Package Short Url https://bioconductor.org/packages/bnem/
Package Downloads Report Download Stats