predictionet
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see predictionet.
Inference for predictive networks designed for (but not limited to) genomic data
Bioconductor version: 3.14
This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is able to generate networks using Bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer networks with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the 'Predictive Networks' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen.
Author: Benjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John Quackenbush
Maintainer: Benjamin Haibe-Kains <bhaibeka at jimmy.harvard.edu>, Catharina Olsen <colsen at ulb.ac.be>
citation("predictionet")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("predictionet")
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("predictionet")| predictionet | R Script | |
| Reference Manual | ||
| README | Text |
Details
| biocViews | GraphAndNetwork, NetworkInference, Software |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | Artistic-2.0 |
| Depends | igraph, catnet |
| Imports | penalized, RBGL, MASS |
| System Requirements | |
| URL | http://compbio.dfci.harvard.edu http://www.ulb.ac.be/di/mlg |
See More
| Suggests | network, minet, knitr |
| 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 | predictionet_1.40.0.tar.gz |
| Windows Binary | |
| macOS 10.13 (High Sierra) | predictionet_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/predictionet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/predictionet |
| Package Short Url | https://bioconductor.org/packages/predictionet/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |