Package: nem
Title: Nested Effects Models to reconstruct phenotypic hierarchies
Version: 2.16.1
Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Christian
        Bender, 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: Froehlich H, Beissbarth T, Tresch A, Kostka D, Jacob J,
        Spang R, Markowetz F: Analyzing gene perturbation screens with
        nested effects models in R and bioconductor, Bioinformatics,
        2008, 24:2549-50.
Maintainer: Holger Froehlich <frohlich@bit.uni-bonn.de>
Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), Rgraphviz (>=
        1.22), plotrix, limma, time (>= 1.0), cluster (>= 1.11),
        statmod
Enhances: doMC
Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
        1.8.1), RColorBrewer, Rgraphviz, stats, utils
Suggests: Biobase (>= 1.10)
LazyLoad: Yes
biocViews: Microarray, Bioinformatics, GraphsAndNetworks, Pathways
URL: http://www.bioconductor.org
License: GPL (>= 2)
Packaged: 2011-04-29 05:24:03 UTC; biocbuild
Built: R 2.13.0; ; 2011-04-29 13:25:06 UTC; windows
