Reconstruction of transcriptional networks and analysis of master regulators

Bioconductor version: Development (3.0)

This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.

Author: Mauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer

Maintainer: Mauro Castro <mauro.a.castro at gmail.com>

To install this package, start R and enter:


Citation (from within R, enter citation("RTN")):


PDF R Script Main vignette: reconstruction and analysis of transcriptional networks in R
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, GeneRegulation, GraphsAndNetwork, Network, NetworkEnrichment, NetworkInference, Software
Version 1.3.3
In Bioconductor since BioC 2.13 (R-3.0)
License Artistic-2.0
Depends R (>= 2.15), methods, igraph
Imports RedeR, minet, snow, limma, data.table, S4Vectors(>= 0.0.2), IRanges(>= 1.99.2), ff, car
Suggests HTSanalyzeR, RUnit, BiocGenerics
System Requirements
URL http://dx.doi.org/10.1038/ncomms3464
Depends On Me Fletcher2013b
Imports Me
Suggests Me

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Package Source RTN_1.3.3.tar.gz
Windows Binary RTN_1.3.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) RTN_1.3.3.tgz
Mac OS X 10.9 (Mavericks) RTN_1.3.3.tgz
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