predictionet

DOI: 10.18129/B9.bioc.predictionet    

Inference for predictive networks designed for (but not limited to) genomic data

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

PDF	R Script	predictionet
PDF		Reference Manual
Text		README

Details

biocViews	GraphAndNetwork, NetworkInference, Software
Version	1.38.0
In Bioconductor since	BioC 2.9 (R-2.14) (10 years)
License	Artistic-2.0
Depends	igraph, catnet
Imports	penalized, RBGL, MASS
LinkingTo
Suggests	network, minet, knitr
SystemRequirements
Enhances
URL	http://compbio.dfci.harvard.edu http://www.ulb.ac.be/di/mlg
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	predictionet_1.38.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	predictionet_1.38.0.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