DESCRIPTION

Package: CNAclinic
Type: Package
Title: A Software Suite for Shallow Sequencing Copy Number Analysis
Version: 1.0
Date: 2017-11-01
Author: Dineika Chandrananda
Maintainer: <dineika.chandrananda@cruk.cam.ac.uk>
Description: This package provides an end-to-end pipeline for copy number aberration (CNA) analysis of shallow coverage whole-genome sequencing (sWGS) data (< 0.5X).
License: GPL
Depends:
    R (>= 3.3.3), methods
Imports:
    graphics,
    stats,
    utils,
    R.utils (>= 1.28.4),
    matrixStats (>= 0.13.1),
    Rsamtools (>= 1.20),
    QDNAseq (>= 1.10.0),
    QDNAseq.hg19,
    HMMcopy,
    copynumber,
    DNAcopy (>= 1.32.0),
    PSCBS,
    CGHbase,
    CGHcall (>= 2.18.0),
    Biobase (>= 2.18.0),
    GenomicRanges, 
    IRanges,
    ggplot2, dplyr,
    data.table,
    scales,
    annotate, org.Hs.eg.db,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    TxDb.Hsapiens.UCSC.hg38.knownGene
biocViews: CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation,
        Preprocessing, QualityControl, Sequencing, Annotation
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests:
    knitr,
    rmarkdown,
    R.cache (>= 0.9.0),
    digest
VignetteBuilder: knitr