Package: nem
Title: Nested Effects Models to reconstruct phenotypic hierarchies
Version: 2.6.0
Author: Florian Markowetz, Holger Froehlich, Achim Tresch, Matthias
        Maneck, Claudio Lottaz, Tim Beissbarth
Description: The package 'nem' allows to reconstruct features of
        pathways from the nested structure of perturbation effects. It
        takes as input (1.) a set of pathway components, which were
        perturbed, and (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.
Reference: Markowetz F, Bloch J, Spang R: Non-transcriptional pathway
        features reconstructed from secondary effects of RNA
        interference, Bioinformatics 2005, 21(21):4026-4032. Froehlich
        H, Fellmann M, Sueltmann H, Poustka A, Beissbarth T: Estimating
        Large Scale Signaling Networks through Nested Effects Models
        from Intervention Effects in Microarray Data. Bioinformatics,
        1, 2008. Froehlich H, Fellmann M, Sueltmann H, Poustka A,
        Beissbarth T: Large Scale Statistical Inference of Signaling
        Pathways from RNAi and Microarray Data, BMC Bioinformatics,
        8:386, 2007.
Maintainer: Florian Markowetz <florian@genomics.princeton.edu>
Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.10), Rgraphviz (>=
        1.10), RBGL (>= 1.8.1), time (>= 1.0), cluster (>= 1.11),
        bootstrap (>= 1.0-20), RColorBrewer, plotrix
Suggests: Biobase (>= 1.10)
biocViews: Microarray, Statistics, GraphsAndNetworks, Pathways
URL: http://www.bioconductor.org
License: GPL (>= 2)
Packaged: Wed Oct 22 03:35:54 2008; biocbuild
Built: R 2.8.0; ; 2008-10-22 10:11:29; windows
