nem

Package: nem
Title: (Dynamic) Nested Effects Models and Deterministic Effects
Propagation Networks to reconstruct phenotypic hierarchies
Version: 2.46.0
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 (>= 3.0)
Enhances: doMC, snow, parallel
Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod,
plotrix, limma
Suggests: Biobase (>= 1.10)
LazyLoad: Yes
biocViews: Microarray, Bioinformatics, GraphsAndNetworks, Pathways,
SystemsBiology, NetworkInference
URL: http://www.bioconductor.org
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-05-04 02:53:47 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'nem' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c MCMC.c -o MCMC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c netlearn.c -o netlearn.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c wrapper.c -o wrapper.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o nem.so MCMC.o netlearn.o wrapper.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/nem/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'nem'
    finding HTML links ... done
    BFSlevel                                html  
    BoutrosRNAi2002                         html  
    Ivanova2006RNAiTimeSeries               html  
    NiederbergerMediator2012                html  
    SCCgraph                                html  
    SahinRNAi2008                           html  
    closest.transitive.greedy               html  
    enumerate.models                        html  
    generateNetwork                         html  
    getDensityMatrix                        html  
    infer.edge.type                         html  
    internal                                html  
    local.model.prior                       html  
    nem                                     html  
    nem.bootstrap                           html  
    nem.calcSignificance                    html  
    nem.consensus                           html  
    nem.cont.preprocess                     html  
    nem.discretize                          html  
    nem.jackknife                           html  
    nemModelSelection                       html  
    network.AIC                             html  
    plot.nem                                html  
    plotEffects                             html  
    prior.EgeneAttach.EB                    html  
    prune.graph                             html  
    quicknem                                html  
    selectEGenes                            html  
    set.default.parameters                  html  
    sim.intervention                        html  
    subsets                                 html  
    transitive.closure                      html  
    transitive.projections                  html  
    transitive.reduction                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nem)
Making 'packages.html' ... done