ddgraph

DOI: 10.18129/B9.bioc.ddgraph    

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ddgraph.

Distinguish direct and indirect interactions with Graphical Modelling

Bioconductor version: Release (3.6)

Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions.

Author: Robert Stojnic

Maintainer: Robert Stojnic <robert.stojnic at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ddgraph")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ddgraph")

 

PDF	R Script	Overview of the 'ddgraph' package
PDF		Reference Manual
Text		NEWS

Details

biocViews	GraphAndNetwork, Software
Version	1.21.0
In Bioconductor since	BioC 2.11 (R-2.15) (5.5 years)
License	GPL-3
Depends	graph, methods, Rcpp
Imports	bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS
LinkingTo	Rcpp
Suggests	Rgraphviz, e1071, ROCR, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	ddgraph_1.21.0.tar.gz
Windows Binary	ddgraph_1.21.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	ddgraph_1.21.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ddgraph
Package Short Url	http://bioconductor.org/packages/ddgraph/
Package Downloads Report	Download Stats