Package: CNVPanelizer
Type: Package
Title: Reliable CNV detection in targeted sequencing applications
Version: 1.16.0
Date: 2019-04-22
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, GenomeInfoDb,
        gplots, reshape2, stringr, testthat, graphics, methods, shiny,
        shinyFiles, shinyjs, grid, openxlsx
License: GPL-3
LazyData: false
biocViews: Classification, Sequencing, Normalization,
        CopyNumberVariation, Coverage
VignetteBuilder: knitr
NeedsCompilation: no
git_url: https://git.bioconductor.org/packages/CNVPanelizer
git_branch: RELEASE_3_9
git_last_commit: 16d1b40
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
Packaged: 2019-05-03 03:38:58 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>
Built: R 3.6.0; ; 2019-05-03 13:05:17 UTC; windows
