Package: PureCN
Type: Package
Title: Copy number calling and SNV classification using targeted short
        read sequencing
Version: 1.2.3
Date: 2016-10-27
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 targeted short read sequencing data, integrates well 
    with standard somatic variant detection pipelines, and has support for 
    tumor samples without matching normal samples.
Depends: R (>= 3.2), DNAcopy, VariantAnnotation (>= 1.14.1)
Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer,
        S4Vectors, data.table, grDevices, graphics, stats, utils,
        SummarizedExperiment, GenomeInfoDb, Rsamtools, Biostrings
Suggests: PSCBS, RUnit, BiocStyle, BiocGenerics, knitr, getopt,
        rtracklayer
VignetteBuilder: knitr
License: Artistic-2.0
biocViews: CopyNumberVariation, Software, Sequencing,
        VariantAnnotation, VariantDetection, Coverage
NeedsCompilation: no
Packaged: 2016-10-29 00:26:46 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-29 04:01:45 UTC; windows
