DESCRIPTION

Package: deepSNV
Maintainer: Moritz Gerstung <mg14@sanger.ac.uk>
License: GPL-3
Title: Detection of subclonal SNVs in deep sequencing data.
biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport
LinkingTo: Rhtslib
Type: Package
LazyLoad: yes
Authors@R: c( person("Niko","Beerenwinkel", role="ths"),
    person("David", "Jones", role = "ctb"),
    person("Inigo", "Martincorena", role = "ctb"),
    person("Moritz","Gerstung",
    email = "mg14@sanger.ac.uk", role= c("aut","cre")) )
Description: This package provides provides quantitative variant callers for
    detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
    experiments. The deepSNV algorithm is used for a comparative setup with a
    control experiment of the same loci and uses a beta-binomial model and a
    likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
    The shearwater algorithm computes a Bayes classifier based on a
    beta-binomial model for variant calling with multiple samples for
    precisely estimating model parameters such as local error rates and
    dispersion and prior knowledge, e.g. from variation data bases such as
    COSMIC.
Version: 1.16.0
URL: http://github.com/mg14/deepSNV
Depends:
    R (>= 2.13.0),
    methods,
    graphics,
    parallel,
    Rhtslib,
    IRanges,
    GenomicRanges,
    SummarizedExperiment,
    Biostrings,
    VGAM,
    VariantAnnotation (>= 1.13.44),
Imports:
    Rhtslib
Suggests:
    RColorBrewer,
    knitr
VignetteBuilder: knitr