birte

Package: birte
Version: 1.8.1
Date: 2015-06-16
Title: Bayesian Inference of Regulatory Influence on Expression (biRte)
Author: Holger Froehlich, contributions by Benedikt Zacher
Maintainer: Holger Froehlich <frohlich@bit.uni-bonn.de>
Depends: R (>= 3.0.0), RcppArmadillo (>= 0.3.6.1), Rcpp
Imports: MASS, limma (>= 3.22.0), glmnet, Biobase, nem
Reference: H. Froehlich, biRte: Bayesian Inference of Context Specific
Regulator Activities and Transcriptional Networks,
Bioinformatics, 2015, in press.
Suggests: knitr
Enhances: Rgraphviz
LinkingTo: RcppArmadillo, Rcpp
NeedsCompilation: yes
SystemRequirements: BLAS, LAPACK
Materials: Please enable BLAS and LAPACK for armadillo library (see
http://arma.sourceforge.net/faq.html). The file config.hpp can
be found under library/RcppArmadillo/include/armadillo_bits.
Description: Expression levels of mRNA molecules are regulated by
different processes, comprising inhibition or activation by
transcription factors and post-transcriptional degradation by
microRNAs. biRte uses regulatory networks of TFs, miRNAs and
possibly other factors, together with mRNA, miRNA and other
available expression data to predict the relative influence of
a regulator on the expression of its target genes. Inference is
done in a Bayesian modeling framework using
Markov-Chain-Monte-Carlo. A special feature is the possibility
for follow-up network reverse engineering between active
regulators.
License: GPL (>= 2)
biocViews: Microarray, Sequencing, GeneExpression, Transcription,
Network, Bayesian, Regression, NetworkInference
LazyLoad: yes
VignetteBuilder: knitr
Packaged: 2016-05-16 05:13:01 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'birte' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c BayesNetwork.cpp -o BayesNetwork.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c getStates.cpp -o getStates.o
Loading required package: Rcpp
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o birte.so BayesNetwork.o getStates.o -llapack -lblas -L/home/ddbj/local/lib64/R/lib -lR
Loading required package: Rcpp
installing to /home/ddbj/local/lib64/R/library/birte/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'birte'
    finding HTML links ... done
    EColiNetwork                            html  
    EColiOxygen                             html  
    TFexpr                                  html  
    birteFitRidge                           html  
    finding level-2 HTML links ... done

    birtePredict                            html  
    birteRun                                html  
    estimateNetwork                         html  
    getPotentialSwaps                       html  
    humanNetwork                            html  
    limmaAnalysis                           html  
    plotConvergence                         html  
    proposeInteractions                     html  
    simplify                                html  
    simulateData                            html  
    suggestThreshold                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (birte)
Making 'packages.html' ... done