lpNet

Linear Programming Model for Network Inference


Bioconductor version: Release (3.19)

lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.

Author: Bettina Knapp, Marta R. A. Matos, Johanna Mazur, Lars Kaderali

Maintainer: Lars Kaderali <lars.kaderali at uni-greifswald.de>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("lpNet")

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("lpNet")
lpNet, network inference with a linear optimization program. PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews NetworkInference, Software
Version 2.36.0
In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)
License Artistic License 2.0
Depends lpSolve, KEGGgraph
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Package Archives

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

Source Package lpNet_2.36.0.tar.gz
Windows Binary (x86_64) lpNet_2.36.0.zip (64-bit only)
macOS Binary (x86_64) lpNet_2.36.0.tgz
macOS Binary (arm64) lpNet_2.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lpNet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lpNet
Bioc Package Browser https://code.bioconductor.org/browse/lpNet/
Package Short Url https://bioconductor.org/packages/lpNet/
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