lpNet
This is the released version of lpNet; for the devel version, see lpNet.
Linear Programming Model for Network Inference
Bioconductor version: Release (3.23)
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("lpNet")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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. | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | NetworkInference, Software |
| Version | 2.44.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | Artistic License 2.0 |
| Depends | lpSolve, KEGGgraph |
| Imports | |
| System Requirements | |
| URL |
See More
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lpNet_2.44.0.tar.gz |
| Windows Binary (x86_64) | lpNet_2.44.0.zip |
| macOS Binary (big-sur-x86_64) | lpNet_2.44.0.tgz |
| macOS Binary (sonoma-arm64) | lpNet_2.44.0.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 |