phenoTest

Package: phenoTest
Type: Package
Title: Tools to test association between gene expression and phenotype
in a way that is efficient, structured, fast and scalable. We
also provide tools to do GSEA (Gene set enrichment analysis)
and copy number variation.
Version: 1.20.0
Date: 2013-05-29
Author: Evarist Planet
Maintainer: Evarist Planet <evarist.planet@epfl.ch>
Description: Tools to test correlation between gene expression and
phenotype in a way that is efficient, structured, fast and
scalable. GSEA is also provided.
License: GPL (>=2)
Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2
Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi,
hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
SNPchip, hgu133a.db, HTSanalyzeR, ellipse
Suggests: GSEABase, KEGG.db, GO.db
Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
LazyLoad: yes
biocViews: Microarray, DifferentialExpression, MultipleComparison,
Clustering, Classification
NeedsCompilation: no
Packaged: 2016-05-04 03:54:59 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'phenoTest' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
  converting help for package 'phenoTest'
    finding HTML links ... done
    ClusterPhenoTest                        html  
    ExpressionPhenoTest                     html  
    barplotSignatures-methods               html  
    barplotSignifSignatures-methods         html  
    epheno-class                            html  
    finding level-2 HTML links ... done

    epheno                                  html  
    epheno2html                             html  
    ephenoGetters                           html  
    eset                                    html  
    eset.genelevel                          html  
    eset2genelevel                          html  
    export2CSV-methods                      html  
    export2CSV                              html  
    findCopyNumber                          html  
    genesInArea                             html  
    getEsPositions                          html  
    getGo                                   html  
    getGseaSignatures                       html  
    getKegg                                 html  
    getVars2test-methods                    html  
    getVars2test                            html  
    gsea                                    html  
    gsea.kegg.go                            html  
    gsea.subset                             html  
    gsea2html                               html  
    gseaData-class                          html  
    gseaSignatures-class                    html  
    gseaSignatures-methods                  html  
    gseaSignatures                          html  
    gseaSignaturesSign-class                html  
    gseaSignaturesVar-class                 html  
    gseaSignificance                        html  
    gseaSignificanceSign-class              html  
    gseaSignificanceVar-class               html  
    heatmapPhenoTest-methods                html  
    heatmapPhenoTest                        html  
    pAdjust-methods                         html  
    pAdjust                                 html  
    pca                                     html  
    phenoTest-package                       html  
    plot.gsea                               html  
    plot.gseaSignatures                     html  
    plots4epheno                            html  
    show-methods                            html  
    smoothCoxph                             html  
    summary.gsea                            html  
    summary.gseaSignificance                html  
    write.html                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* DONE (phenoTest)
Making 'packages.html' ... done