lpNet

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see lpNet.

Linear Programming Model for Network Inference


Bioconductor version: 3.10

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>

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

Installation

To install this package, start R (version "3.6") 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 2.18.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License Artistic License 2.0
Depends lpSolve, nem
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Package Archives

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

Source Package lpNet_2.18.0.tar.gz
Windows Binary lpNet_2.18.0.zip
Mac OS X 10.11 (El Capitan) lpNet_2.18.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive