RTN - Reconstruction and Analysis of Transcriptional Networks

Reconstruction and Analysis of Transcriptional Networks

This package provides classes and methods for transcriptional network inference and 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.

RTN comes with two data packages from Fletcher*, Castro* et al (Nat Comm 2013):

Download

To install this package and the corresponding data packages directly in R type:

	source("http://bioconductor.org/biocLite.R")
	biocLite("RTN")
	biocLite("Fletcher2013a")
	biocLite("Fletcher2013b")
	

References

 

R

Developers

Download

RTN is available from bioconductor.org

The data and analysis of FGFR2 signaling and breast cancer risk (Fletcher, Castro et al 2013) are available as packages Fletcher2013a and Fletcher2013b from Bioconductor.

BioConductor

Download statistics

Download stats

Other packages

Software
  • BaalChIP - allele-specific TF binding
  • BitPhylogeny - infer intra-tumor phylogenies
  • CRImage - tumor image analysis
  • DANCE - subtype specific drivers of cancer
  • GoIFISH - single cell IFISH analysis
  • HTSanalyzeR - functional annotation
  • lol - lots of lassos
  • MEDICC - intra-patient copy number comparison
  • nem - nested effects models
  • OncoNEM - oncogenetic NEMs
  • PAN - posterior associa- tion networks
  • RedeR - graph visualiza- tion and analysis
  • RTN - network recon- struction and analysis
  • SANTA - spatial analysis of network associations
  • VULCAN - co-factors from CHiP-seq data
Data @ Bioconductor