ddgraph

Distinguish direct and indirect interactions with Graphical Modelling

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("ddgraph")

To cite this package in a publication, start R and enter:

    citation("ddgraph")

Documentation

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

Details

biocViews GraphAndNetwork, Software
Version 1.9.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL-3
Depends graph, methods, Rcpp
Imports bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS
Suggests Rgraphviz, e1071, ROCR, testthat
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ddgraph_1.9.0.tar.gz
Windows Binary ddgraph_1.9.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ddgraph_1.9.0.tgz
Mac OS X 10.9 (Mavericks)
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