Package: SomatiCA
Type: Package
Title: SomatiCA: identifying, characterizing, and quantifying somatic
        copy number aberrations from cancer genome sequencing
Version: 1.4.0
Date: 2013-06-13
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
biocViews: Bioinformatics, Sequencing, CopyNumberVariants
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)
Packaged: 2013-10-15 08:13:38 UTC; biocbuild
Built: R 3.0.2; ; 2013-10-15 16:09:19 UTC; windows
