R package for Nested Effects Model Object-oriented

Nested Effect Models (NEMs) are a group of graphical models for reconstruction of cellular signalling pathways based on downstream effects after systematic perturbations of signalling genes. They have been successfully used in many real biological applications.

Features

• The Nested Effects Model Object-oriented (NEMO) package for R is designed for all existing NEMs and tries to organize them in an object-oriented framework, facilitating a clear understanding of the intrinsic relationships among them. In addition, we are developing an extended model of NEM to infer dynamic signalling pathways in my Lab. The structure of NEMO will allow an easy extension for our future models.
• Another feature of NEMO is that its network graphic engine is based on another package in R-forge called 'IGIR', which provides a much better network visualization power than any other existing graphic engines in R.

Download

You can download the latest version from here.

References

• F. Markowetz, J. Bloch, R. Spang. Non-transcriptional Pathway Features Reconstructed from Secondary Effects of RNA Interference. Bioinformatics 2005 21: 4026-4032
• F. Markowetz, D. Kostka, O.G. Troyanskaya, R. Spang. Nested Effects Models for High-Dimensional Phenotyping Screens. Bioinformatics 2007 23(13):i305-i312