nem - estimating Nested Effects Models from data

Nested Effects Model

The R/Bioconductor package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input

  1. a set of perturbed pathway components
  2. high-dimensional phenotypic readout of these perturbations (e.g. gene expression or morphological profiles).

The output is a directed graph representing the phenotypic hierarchy. The package contains an example dataset on Drosophila immune response and a vignette explaining its application.

Download and Installation

You can download the newest release from the package's Bioconductor page.

To install this package directly in R type:



The software package combines the methods introduced in several papers:



  • Florian Markowetz
  • Holger Fröhlich
  • Achim Tresch
  • Christian Bender
  • Matthias Maneck
  • Claudio Lottaz
  • Tim Beissbarth
  • and others ...


You can download the newest release from the package's Bioconductor page.


Download statistics

Download stats

Other packages

  • 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