The package 'pcnem' allows to reconstruct networks from probabilistically modelled combinatorial perturbations. It takes as input (1.) a set of pathway components, which were perturbed, (2.) a perturbation map defining the perturbation probabilities of each component, and (3.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed acyclic graph representing the phenotypic hierarchy.
Package details 


Author  Sumana Srivatsa, Niko Beerenwinkel 
Bioconductor views  Bioinformatics GraphsAndNetworks Microarray NetworkInference Pathways SystemsBiology 
Maintainer  Sumana Srivatsa <[email protected]> 
License  GPL (>= 2) 
Version  2.46.0 
URL  http://www.bioconductor.org 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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