MMDiff2

Package: MMDiff2
Description: This package detects statistically significant differences between
read enrichment profiles in different ChIP-Seq samples. To take advantage of
shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).
Type: Package
Title: Statistical Testing for ChIP-Seq data sets
Version: 1.0.2
Authors@R: c(
person("Gabriele", "Schweikert", role = c("cre", "aut"), email = "gschweik@staffmail.ed.ac.uk"),
person("David", "Kuo", role = "aut", email = "dkuo@cbio.mskcc.org"))
Depends: R (>= 3.3), Rsamtools, Biobase,
biocViews: ChIPSeq, DifferentialPeakCalling, Sequencing, Software
License: Artistic-2.0
Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
ImportFrom: utils txtProgressBar setTxtProgressBar read.csv
Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Collate: 'DBAmmd-Class.R' 'AllGenerics.R' 'DBAmmd-Accessors.R'
'DBAmmd-Showmethods.R' 'DBAmmd-internal.R' 'MMDiff2_data.R'
'compDists.R' 'compHists.R' 'compPvals.R' 'createPeakMatrix.R'
'estimateFragmentCenters.R' 'getPeakReads.R' 'helperFcts.R'
'plotDISTS4Peak.R' 'plotDists.R' 'plotPeak.R' 'reportResults.R'
'runShinyMMDiff2.R' 'server.R' 'ui.R'
NeedsCompilation: no
Packaged: 2016-05-16 06:13:51 UTC; biocbuild
Author: Gabriele Schweikert [cre, aut],
David Kuo [aut]
Maintainer: Gabriele Schweikert <gschweik@staffmail.ed.ac.uk>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MMDiff2' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MMDiff2'
    finding HTML links ... done
    Cfp1-Peaks                              html  
    DBAmmd-Accessors                        html  
    DBAmmd-class                            html  
    MMD                                     html  
    compDists                               html  
    compHists                               html  
    compPvals                               html  
    estimateFragmentCenters                 html  
    getPeakReads                            html  
    mm9-Genes                               html  
    myGeneric                               html  
    plotDISTS4Peak                          html  
    plotDists                               html  
    plotPeak                                html  
    reportResults                           html  
    runShinyMMDiff2                         html  
    server.MMDiff2                          html  
    ui.MMDiff2                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MMDiff2)
Making 'packages.html' ... done