Package: deepSNV
Imports: Rsamtools
Maintainer: Moritz Gerstung <moritz.gerstung@sanger.ac.uk>
License: GPL-3
Title: Detection of subclonal SNVs in deep sequencing experiments.
biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport
LinkingTo: Rsamtools
Type: Package
LazyLoad: yes
Author: Moritz Gerstung and Niko Beerenwinkel
Description: This package provides provides a 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 new shearwater algorithm (beta) 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: 1.10.0
URL: http://www.cbg.ethz.ch/software/deepSNV
Depends: R (>= 2.13.0), Rsamtools (>= 1.4.3), GenomicRanges, IRanges,
        Biostrings, VGAM, methods, graphics, VariantAnnotation (>=
        1.5.0), parallel
Suggests: RColorBrewer, knitr
VignetteBuilder: knitr
Collate: 'deepSNV-class.R' 'deepSNV-experimental.R'
        'deepSNV-functions.R' 'deepSNV-generics.R' 'deepSNV-methods.R'
        'deepSNV-misc.R' 'deepSNV-package.R' 'shearwater-functions.R'
Packaged: 2014-04-12 09:51:48 UTC; biocbuild
Built: R 3.1.0; i386-w64-mingw32; 2014-04-12 12:52:38 UTC; windows
Archs: i386, x64
