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 (from within R, enter 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 PDF R Script
Reference Manual PDF
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