Package: nem
Title: (Dynamic) Nested Effects Models and Deterministic Effects
        Propagation Networks to reconstruct phenotypic hierarchies
Version: 2.36.0
Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Theresa Niederberger, 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.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). 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), plotrix, limma,
        cluster (>= 1.11), statmod, Hmisc, Rgraphviz
Enhances: doMC, Rglpk
Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
        1.8.1), RColorBrewer, stats, utils, Rgraphviz
Suggests: Biobase (>= 1.10)
LazyLoad: Yes
biocViews: Microarray, Bioinformatics, GraphsAndNetworks, Pathways
URL: http://www.bioconductor.org
License: GPL (>= 2)
Packaged: 2013-04-11 03:09:31 UTC; biocbuild
Built: R 3.0.0; x86_64-apple-darwin10.8.0; 2013-04-11 08:02:19 UTC; unix
