Package: SomatiCA
Type: Package
Title: SomatiCA: identifying, characterizing, and quantifying somatic
        copy number aberrations from cancer genome sequencing
Version: 1.10.0
Date: 2013-10-29
Author: Mengjie Chen <mengjie.chen@yale.edu>, Hongyu Zhao
        <hongyu.zhao@yale.edu>
Maintainer: Mengjie Chen <mengjie.chen@yale.edu>
Imports: foreach, lars, sn, DNAcopy, methods, rebmix, GenomicRanges,
        IRanges
Depends: R (>= 2.14.0), lars, DNAcopy, foreach, methods, rebmix,
        GenomicRanges, IRanges, doParallel
Enhances: sn, SomatiCAData
Description: SomatiCA is a software suite that is capable of
        identifying, characterizing, and quantifying somatic CNAs from
        cancer genome sequencing. First, it uses read depths and lesser
        allele frequencies (LAF) from mapped short sequence reads to
        segment the genome and identify candidate CNAs. Second,
        SomatiCA estimates the admixture rate from the relative
        copy-number profile of tumor-normal pair by a Bayesian finite
        mixture model. Third, SomatiCA quantifies absolute somatic
        copy-number and subclonality for each genomic segment to guide
        its characterization. Results from SomatiCA can be further
        integrated with single nucleotide variations (SNVs) to get a
        better understanding of the tumor evolution.
License: GPL (>=2)
biocViews: Sequencing, CopyNumberVariation
Packaged: 2014-10-14 04:17:26 UTC; biocbuild
Built: R 3.1.1; ; 2014-10-14 13:35:46 UTC; windows
