CNVPanelizer

Package: CNVPanelizer
Type: Package
Title: Reliable CNV detection in targeted sequencing applications
Version: 1.2.2
Date: 2016-03-18
Authors@R: c(
person("Cristiano", "Oliveira", email = "cristiano.oliveira@med.uni-heidelberg.de", role = c("aut")),
person("Thomas", "Wolf", email = "thomas_wolf71@gmx.de", role = c("aut", "cre")),
person("Albrecht", "Stenzinger", email = "albrecht.stenzinger@med.uni-heidelberg.de", role = c("ctb")),
person("Volker", "Endris", email = "volker.endris@med.uni-heidelberg.de", role = c("ctb")),
person("Nicole", "Pfarr", email = "nicole.pfarr@med.uni-heidelberg.de", role = c("ctb")),
person("Benedikt", "Brors", email = "b.brors@dkfz.de", role = c("ths")),
person("Wilko", "Weichert", email = "wilko.weichert@med.uni-heidelberg.de", role = c("ths")))
Description: A method that allows for the use of a collection of non-matched
normal tissue samples. Our approach uses a non-parametric bootstrap
subsampling of the available reference samples to estimate the distribution
of read counts from targeted sequencing. As inspired by random forest, this
is combined with a procedure that subsamples the amplicons associated with
each of the targeted genes. The obtained information allows us to reliably
classify the copy number aberrations on the gene level.
Depends: R (>= 3.2.0), GenomicRanges
Suggests: knitr, RUnit, BiocGenerics
Imports: S4Vectors, grDevices, stats, utils, NOISeq, IRanges,
Rsamtools, exomeCopy, foreach, ggplot2, plyr, openxlsx
License: GPL-3
LazyData: false
biocViews: Classification, Sequencing, Normalization,
CopyNumberVariation, Coverage
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-16 05:32:48 UTC; biocbuild
Author: Cristiano Oliveira [aut],
Thomas Wolf [aut, cre],
Albrecht Stenzinger [ctb],
Volker Endris [ctb],
Nicole Pfarr [ctb],
Benedikt Brors [ths],
Wilko Weichert [ths]
Maintainer: Thomas Wolf <thomas_wolf71@gmx.de>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CNVPanelizer' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVPanelizer'
    finding HTML links ... done
    Background                              html  
    BedToGenomicRanges                      html  
    BootList                                html  
    CNVPanelizer-package                    html  
    CombinedNormalizedCounts                html  
    IndexMultipleBams                       html  
    PlotBootstrapDistributions              html  
    ReadCountsFromBam                       html  
    ReadXLSXToList                          html  
    ReportTables                            html  
    WriteListToXLSX                         html  
    referenceReadCounts                     html  
    sampleReadCounts                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNVPanelizer)
Making 'packages.html' ... done