Package: cn.mops
Maintainer: Guenter Klambauer <cn.mops@bioinf.jku.at>
Author: Guenter Klambauer
License: LGPL (>= 2.0)
Type: Package
Title: cn.mops - Mixture of Poissons for CNV detection in NGS data
Description: cn.mops (Copy Number estimation by a Mixture
    Of PoissonS) is a data processing pipeline for copy
    number variations and aberrations (CNVs and CNAs) from
    next generation sequencing (NGS) data. The package
    supplies functions to convert BAM files into read count
    matrices or genomic ranges objects, which are the input
    objects for cn.mops. cn.mops models the depths of
    coverage across samples at each genomic position.
    Therefore, it does not suffer from read count biases
    along chromosomes. Using a Bayesian approach, cn.mops
    decomposes read variations across samples into integer
    copy numbers and noise by its mixture components and
    Poisson distributions, respectively. cn.mops guarantees
    a low FDR because wrong detections are indicated by high
    noise and filtered out. cn.mops is very fast and
    written in C++.
biocViews: HighThroughputSequencing, Sequencing, Bioinformatics,
        CopyNumberVariants, Homo_sapiens, CellBiology,
        HighTroughputSequencingData, HapMap, Genetics
Version: 1.8.9
Date: 2014-14-02
URL: http://www.bioinf.jku.at/software/cnmops/cnmops.html
Depends: R (>= 2.12), BiocGenerics, Biobase, IRanges, GenomicRanges
Imports: methods, graphics, BiocGenerics, IRanges, Rsamtools,
Suggests: snow, DNAcopy
LazyLoad: yes
Collate: 'AllClasses.R' 'cn.mops.R' 'getReadCountsFromBAM.R'
        'normalizeChromosomes.R' 'normalizeGenome.R' 'plot-methods.R'
        'show-methods.R' 'segment.R' 'zzz.R' 'AllGenerics.R'
        'methodsAccess.R' 'getSegmentReadCountsFromBAM.R'
        'haplocn.mops.R' 'segPlot.R' 'exomecn.mops.R'
        'calcIntegerCopyNumbers.R' 'makeRobustCNVR.R'
        'referencecn.mops.R' 'calcFractionalCopyNumbers.R'
        'singlecn.mops.R'
Packaged: 2014-03-12 07:57:06 UTC; biocbuild
Built: R 3.0.3; i386-w64-mingw32; 2014-03-12 10:01:18 UTC; windows
Archs: i386, x64
