edge

Package: edge
Type: Package
Title: Extraction of Differential Gene Expression
Date: 2015-04-15
Version: 2.4.2
Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
<ajbass@princeton.edu>
biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
Regression, GeneExpression, DataImport
Description: The edge package implements methods for carrying out differential
expression analyses of genome-wide gene expression studies. Significance testing
using the optimal discovery procedure and generalized likelihood ratio tests
(equivalent to F-tests and t-tests) are implemented for general study designs.
Special functions are available to facilitate the analysis of common study
designs, including time course experiments. Other packages such as snm, sva,
and qvalue are integrated in edge to provide a wide range of tools for gene
expression analysis.
VignetteBuilder: knitr
Imports: methods, splines, sva, snm, jackstraw, qvalue (>= 1.99.0), MASS
Suggests: testthat, knitr, ggplot2, reshape2
Depends: R (>= 3.1.0), Biobase
URL: https://github.com/jdstorey/edge
BugReports: https://github.com/jdstorey/edge/issues
LazyData: true
License: MIT + file LICENSE
NeedsCompilation: yes
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:28:06 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'edge' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c edge-init.c -o edge-init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c edgeKLODP.c -o edgeKLODP.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o edge.so edge-init.o edgeKLODP.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/edge/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'edge'
    finding HTML links ... done
    apply_jackstraw                         html  
    finding level-2 HTML links ... done

    apply_qvalue                            html  
    apply_snm                               html  
    apply_sva                               html  
    betaCoef                                html  
    build_models                            html  
    build_study                             html  
    deFit-class                             html  
    deSet-class                             html  
    deSet                                   html  
    edge                                    html  
    endotoxin                               html  
    fitFull                                 html  
    fitNull                                 html  
    fit_models                              html  
    fullMatrix                              html  
    fullModel                               html  
    gibson                                  html  
    individual                              html  
    kidney                                  html  
    kl_clust                                html  
    lrt                                     html  
    nullMatrix                              html  
    nullModel                               html  
    odp                                     html  
    qvalueObj                               html  
    resFull                                 html  
    resNull                                 html  
    sType                                   html  
    show                                    html  
    summary                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edge)
Making 'packages.html' ... done