regioneR

Package: regioneR
Type: Package
Title: Association analysis of genomic regions based on permutation
tests
Version: 1.4.2
Date: 2016-04-06
Author: Anna Diez-Villanueva <adiez@imppc.org>, Roberto Malinverni
<rmalinverni@carrerasresearch.org> and Bernat Gel <bgel@imppc.org>
Maintainer: Bernat Gel <bgel@imppc.org>
Description: regioneR offers a statistical framework based on
customizable permutation tests to assess the association
between genomic region sets and other genomic features.
License: Artistic-2.0
Depends: memoise, GenomicRanges, BSgenome, rtracklayer, parallel
Imports: memoise, GenomicRanges, BSgenome, rtracklayer, parallel,
graphics, stats, utils, GenomeInfoDb, IRanges
Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked,
testthat
VignetteBuilder: knitr
biocViews: Genetics, ChIPSeq, DNASeq, MethylSeq, CopyNumberVariation
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:22:11 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'regioneR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'regioneR'
    finding HTML links ... done
    characterToBSGenome                     html  
    finding level-2 HTML links ... done

    circularRandomizeRegions                html  
    commonRegions                           html  
    createFunctionsList                     html  
    createRandomRegions                     html  
    emptyCacheRegioneR                      html  
    extendRegions                           html  
    filterChromosomes                       html  
    getChromosomesByOrganism                html  
    getGenome                               html  
    getGenomeAndMask                        html  
    getMask                                 html  
    joinRegions                             html  
    listChrTypes                            html  
    localZScore                             html  
    maskFromBSGenome                        html  
    meanDistance                            html  
    meanInRegions                           html  
    mergeRegions                            html  
    numOverlaps                             html  
    overlapGraphicalSummary                 html  
    overlapPermTest                         html  
    overlapRegions                          html  
    permTest                                html  
    plot.localZScoreResults                 html  
    plot.localZScoreResultsList             html  
    plot.permTestResults                    html  
    plot.permTestResultsList                html  
    plotRegions                             html  
    print.permTestResults                   html  
    randomizeRegions                        html  
    recomputePermTest                       html  
    resampleRegions                         html  
    splitRegions                            html  
    subtractRegions                         html  
    summary.permTestResults                 html  
    summary.permTestResultsList             html  
    toDataframe                             html  
    toGRanges                               html  
    uniqueRegions                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)
Making 'packages.html' ... done