An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.
Package details 


Author  Yiming Zuo <yimingzuo@gmail.com>, Kian Ghaffari <kg.ghaffari@gmail.com>, Zhenzhi Li <zzrickli@gmail.com> 
Bioconductor views  BiologicalQuestion DifferentialExpression ImmunoOncology MassSpectrometry Metabolomics ResearchField Software StatisticalMethod 
Maintainer  Ressom group <hwr@georgetown.edu>, Yiming Zuo <yimingzuo@gmail.com> 
License  Artistic2.0 
Version  2.4.0 
URL  http://github.com/ressomlab/INDEED 
Package repository  View on Bioconductor 
Installation 
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