PureCN

Package: PureCN
Type: Package
Title: Estimating tumor purity, ploidy, LOH, and SNV status using
hybrid capture NGS data
Version: 1.0.3
Date: 2016-06-04
Author: Markus Riester
Maintainer: Markus Riester <markus.riester@novartis.com>
Description: This package estimates tumor purity, copy number, loss of
heterozygosity (LOH), and status of single nucleotide variants (SNVs).
PureCN is designed for hybrid capture sequencing data, integrates
well with standard somatic variant detection pipelines,
and has support for tumor samples without matching normal samples.
Depends: R (>= 3.3), DNAcopy, VariantAnnotation (>= 1.14.1)
Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer,
S4Vectors, data.table, grDevices, graphics, stats, utils,
SummarizedExperiment, GenomeInfoDb
Suggests: PSCBS, RUnit, BiocStyle, BiocGenerics, knitr
VignetteBuilder: knitr
License: Artistic-2.0
biocViews: CopyNumberVariation, Software, Sequencing,
VariantAnnotation, VariantDetection
NeedsCompilation: no
Packaged: 2016-06-06 06:04:50 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'PureCN' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'PureCN'
    finding HTML links ... done
    chr.hash                                html  
    correctCoverageBias                     html  
    createCurationFile                      html  
    createExonWeightFile                    html  
    createNormalDatabase                    html  
    createSNPBlacklist                      html  
    filterVcfBasic                          html  
    filterVcfMuTect                         html  
    findBestNormal                          html  
    findFocal                               html  
    getSexFromCoverage                      html  
    plotAbs                                 html  
    plotBestNormal                          html  
    poolCoverage                            html  
    predictSomatic                          html  
    purecn.example.output                   html  
    readCoverageGatk                        html  
    readCurationFile                        html  
    runAbsoluteCN                           html  
    segmentationCBS                         html  
    segmentationPSCBS                       html  
    setPriorVcf                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PureCN)
Making 'packages.html' ... done