DESCRIPTION

Package: deepSNV
Maintainer: Moritz Gerstung <moritz.gerstung@ebi.ac.uk>
License: GPL-3
Title: Detection of subclonal SNVs in deep sequencing data.
biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport
LinkingTo: Rhtslib (>= 1.13.1)
Type: Package
LazyLoad: yes
Authors@R: c( person("Niko","Beerenwinkel", role="ths"),
    person("Raul", "Alcantara", role="ctb"),
    person("David", "Jones", role = "ctb"),
    person("John", "Marshall", role = "ctb"),
    person("Inigo", "Martincorena", role = "ctb"),
    person("Moritz","Gerstung",
    email = "moritz.gerstung@ebi.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: 1.43.6
Depends:
    R (>= 2.13.0),
    methods,
    graphics,
    parallel,
    IRanges,
    GenomicRanges,
    SummarizedExperiment,
    Biostrings,
    VGAM,
    VariantAnnotation (>= 1.27.6),
Imports:
    Rhtslib
Suggests:
    RColorBrewer,
    knitr,
    rmarkdown
VignetteBuilder: knitr
SystemRequirements: GNU make
RoxygenNote: 7.0.2