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:

	source("http://bioconductor.org/biocLite.R")
	biocLite("nem")
	

References:

The software package combines the methods introduced in several papers:

R

Developers

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

Download

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

BioConductor

Download statistics

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Data @ Bioconductor