QDNAseq

Package: QDNAseq
Version: 1.8.0
Date: 2016-03-22
Title: Quantitative DNA sequencing for chromosomal aberrations
Author: Ilari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut]
Maintainer: Daoud Sie <d.sie@vumc.nl>
Depends: R (>= 3.1.0)
Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase
(>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0),
GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>=
0.15.0), R.utils (>= 2.2.0), Rsamtools (>= 1.20),
Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>=
0.6.8), GenomeInfoDb (>= 1.6.0), future (>= 0.12.0), R.cache
(>= 0.12.0)
Description: Quantitative DNA sequencing for chromosomal aberrations.
The genome is divided into non-overlapping fixed-sized bins, number of
sequence reads in each counted, adjusted with a simultaneous
two-dimensional loess correction for sequence mappability and GC
content, and filtered to remove spurious regions in the genome.
Downstream steps of segmentation and calling are also implemented via
packages DNAcopy and CGHcall, respectively.
biocViews: CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation,
Preprocessing, QualityControl, Sequencing
License: GPL
URL: https://github.com/ccagc/QDNAseq
BugReports: https://github.com/ccagc/QDNAseq/issues
NeedsCompilation: no
Packaged: 2016-05-04 05:22:15 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'QDNAseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'QDNAseq'
    finding HTML links ... done
    LGG150                                  html  
    QDNAseq-defunct                         html  
    QDNAseq-package                         html  
    QDNAseqCopyNumbers                      html  
    QDNAseqReadCounts                       html  
    QDNAseqSignals                          html  
    addPhenodata                            html  
    applyFilters                            html  
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/applyFilters.Rd:31: missing file link 'madDiff'
    binReadCounts                           html  
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/binReadCounts.Rd:28: missing file link 'AnnotatedDataFrame'
    callBins                                html  
    compareToReference                      html  
    correctBins                             html  
    createBins                              html  
    estimateCorrection                      html  
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/estimateCorrection.Rd:43: missing file link 'madDiff'
    exportBins                              html  
    finding level-2 HTML links ... done

    frequencyPlot                           html  
    getBinAnnotations                       html  
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/getBinAnnotations.Rd:43: missing file link 'AnnotatedDataFrame'
    highlightFilters                        html  
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/highlightFilters.Rd:32: missing file link 'madDiff'
    isobarPlot                              html  
    makeCgh                                 html  
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/makeCgh.Rd:37: missing file link 'cghRaw'
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/makeCgh.Rd:38: missing file link 'cghSeg'
Rd warning: /tmp/RtmpnZKuvO/R.INSTALL57d07ca461fc/QDNAseq/man/makeCgh.Rd:39: missing file link 'cghCall'
    noisePlot                               html  
    normalizeBins                           html  
    normalizeSegmentedBins                  html  
    plot                                    html  
    poolRuns                                html  
    segmentBins                             html  
    smoothOutlierBins                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (QDNAseq)
Making 'packages.html' ... done