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: 1.56.0
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
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:10:14 UTC
RemoteUrl: https://github.com/bioc/deepSNV
RemoteRef: RELEASE_3_22
RemoteSha: 50518b9496a0cd81004b2194d92eb541b59063bd
NeedsCompilation: yes
Packaged: 2026-01-26 08:51:39 UTC; root
Author: Niko Beerenwinkel [ths],
  Raul Alcantara [ctb],
  David Jones [ctb],
  John Marshall [ctb],
  Inigo Martincorena [ctb],
  Moritz Gerstung [aut, cre]
Built: R 4.5.2; x86_64-w64-mingw32; 2026-01-26 08:53:45 UTC; windows
Archs: x64
