DChIPRep

Package: DChIPRep
Title: DChIPRep - Analysis of chromatin modification ChIP-Seq data with
replication
Version: 1.2.3
Authors@R: c(person("Bernd", "Klaus", email = "bernd.klaus@embl.de",
role = c("aut", "cre")),
person("Christophe", "Chabbert", email
= "christophe.chabbert@embl.de", role = "aut"),
person("Sebastian", "Gibb", role="ctb",
email="mail@sebastiangibb.de"))
Description: The DChIPRep package implements a methodology to assess
differences between chromatin modification profiles in
replicated ChIP-Seq studies as described in Chabbert et. al -
http://www.dx.doi.org/10.15252/msb.20145776. A detailed description of
the method is given in the software paper at https://doi.org/10.7717/peerj.1981
Depends: R (>= 3.3), DESeq2
Imports: methods, stats, utils, ggplot2, fdrtool, reshape2,
GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr,
assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno
License: MIT + file LICENCE
LazyData: true
Suggests: mgcv, testthat, BiocStyle, knitr, rmarkdown
Collate: 'AllClasses.R' 'AllGenerics.R' 'DChipRep.R' 'dataImport.R'
'dataImportsoGGi.R' 'documentData.R' 'methods.R'
'plottingFunctions.R' 'runTesting.R'
VignetteBuilder: knitr
biocViews: Sequencing, ChIPSeq
SystemRequirements: Python 2.7, HTSeq (>= 0.6.1), numpy, argparse, sys
NeedsCompilation: no
Author: Bernd Klaus [aut, cre], Christophe Chabbert [aut], Sebastian Gibb [ctb]
Maintainer: Bernd Klaus <bernd.klaus@embl.de>
RoxygenNote: 5.0.1
Packaged: 2016-06-01 05:46:34 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DChIPRep' ...
** R
** data
*** moving datasets to lazyload DB

Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DChIPRep'
    finding HTML links ... done
    DChIPRep                                html  
    DChIPRepResults                         html  
    DESeq2Data                              html  
    FDRresults                              html  
    TSS_galonska                            html  
    chip_galonska                           html  
    exampleChipData                         html  
    exampleInputData                        html  
    exampleSampleTable                      html  
    getMATfromDataFrame                     html  
    importData                              html  
    importDataFromMatrices                  html  
    importData_soGGi                        html  
Rd warning: /tmp/Rtmpenbo85/R.INSTALL49d411abf4c/DChIPRep/man/importData_soGGi.Rd:36: missing file link 'regionPlot'
Rd warning: /tmp/Rtmpenbo85/R.INSTALL49d411abf4c/DChIPRep/man/importData_soGGi.Rd:14: missing file link 'GenomicRanges-class'
Rd warning: /tmp/Rtmpenbo85/R.INSTALL49d411abf4c/DChIPRep/man/importData_soGGi.Rd:27: missing file link 'regionPlot'
Rd warning: /tmp/Rtmpenbo85/R.INSTALL49d411abf4c/DChIPRep/man/importData_soGGi.Rd:65: missing file link 'regionPlot'
    input_galonska                          html  
    plotProfiles                            html  
    plotSignificance                        html  
    resultsDChIPRep                         html  
    runTesting                              html  
    sample_table_galonska                   html  
    show                                    html  
    summarizeCountsPerPosition              html  
    testData                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
* DONE (DChIPRep)
Making 'packages.html' ... done