Package: nem
Title: Nested Effects Models to reconstruct phenotypic hierarchies
Version: 2.4.0
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. Proc. German
        Conf. Bioinformatics (GCB), pp. 45 - 54, 2007. 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)
Suggests: Biobase (>= 1.10)
biocViews: Microarray, Statistics, GraphsAndNetworks, Pathways
URL: http://www.bioconductor.org
License: GPL (>= 2)
Packaged: Mon May 12 03:46:39 2008; biocbuild
Built: R 2.7.0; ; 2008-05-12 08:37:46; windows
