DOI: 10.18129/B9.bioc.RTN    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see RTN.

Reconstruction of transcriptional networks and analysis of master regulators

Bioconductor version: 3.7

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>

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biocViews GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, NetworkEnrichment, NetworkInference, SNP, Software
Version 2.4.6
In Bioconductor since BioC 2.13 (R-3.0) (5 years)
License Artistic-2.0
Depends R (>= 3.3.3), methods
Imports RedeR, minet, viper, mixtools, snow, limma, data.table, IRanges, igraph, S4Vectors
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
URL http://dx.doi.org/10.1038/ncomms3464
Depends On Me Fletcher2013b, RTNduals, RTNsurvival
Imports Me
Suggests Me geneplast
Links To Me
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