netClass

Package: netClass
Version: 1.2.1
Date: 2013-12-03
Title: netClass: An R Package for Network-Based Biomarker Discovery
Author: Yupeng Cun
Maintainer: Yupeng Cun <yupeng.cun@gmail.com>
Description: netClass is an R package for network-based feature (gene)
selection for biomarkers discovery via integrating biological
information. This package adapts the following 5 algorithms
for classifying and predicting gene expression data using prior
knowledge: 1) average gene expression of pathway (aep); 2)
pathway activities classification (PAC); 3) Hub network
Classification (hubc); 4) filter via top ranked genes (FrSVM);
5) network smoothed t-statistic (stSVM).
Depends: R (>= 2.14), kernlab
Imports: AnnotationDbi, Matrix, ROCR, graph, igraph, samr
Suggests: parallel, Biobase, KEGG.db, pathClass
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-12-03 21:27:02 UTC; cun
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-03 22:44:46

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'netClass' ...
** package 'netClass' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'netClass'
    finding HTML links ... done
    EN2SY                                   html  
    Gs2                                     html  
    ad.matrix                               html  
    calc.diffusionKernelp                   html  
    classify.aep                            html  
    classify.frsvm                          html  
    classify.hubc                           html  
    classify.pac                            html  
    classify.stsvm                          html  
    cv.aep                                  html  
    cv.frsvm                                html  
    cv.hubc                                 html  
    cv.pac                                  html  
    cv.stsvm                                html  
    expr                                    html  
    getGeneRanking                          html  
    getGraphRank                            html  
    netClass-package                        html  
    pGeneRANK                               html  
    pOfHubs                                 html  
    predictAep                              html  
    predictFrsvm                            html  
    predictHubc                             html  
    predictPac                              html  
    predictStsvm                            html  
    probeset2pathway                        html  
    probeset2pathwayTrain                   html  
    probeset2pathwayTst                     html  
    train.aep                               html  
    train.frsvm                             html  
    train.hubc                              html  
    train.pac                               html  
    train.stsvm                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (netClass)
Making 'packages.html' ... done