bnem
Training of logical models from indirect measurements of perturbation experiments
Bioconductor version: Release (3.20)
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("bnem")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneRegulation, Network, NetworkInference, Pathways, Preprocessing, Software, SystemsBiology |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
| 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | bnem_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | bnem_1.14.0.tgz |
| macOS Binary (arm64) | bnem_1.13.0.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 |