lpNet

DOI: 10.18129/B9.bioc.lpNet    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see lpNet.

Linear Programming Model for Network Inference

Bioconductor version: 3.9

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 tu-dresden.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	NetworkInference, Software
Version	2.16.0
In Bioconductor since	BioC 2.12 (R-3.0) (6.5 years)
License	Artistic License 2.0
Depends	lpSolve, nem
Imports
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Build Report

Package Archives

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

Source Package	lpNet_2.16.0.tar.gz
Windows Binary	lpNet_2.16.0.zip
Mac OS X 10.11 (El Capitan)	lpNet_2.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/lpNet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/lpNet
Package Short Url	https://bioconductor.org/packages/lpNet/
Package Downloads Report	Download Stats