SomatiCA

SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

Bioconductor version: Development (3.0)

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.

Author: Mengjie Chen <mengjie.chen at yale.edu>, Hongyu Zhao <hongyu.zhao at yale.edu>

Maintainer: Mengjie Chen <mengjie.chen at yale.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("SomatiCA")

To cite this package in a publication, start R and enter:

    citation("SomatiCA")

Documentation

PDF R Script SomatiCA Vignette
PDF SomatiCAUserGuide.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>=2)
Depends R (>= 2.14.0), lars, DNAcopy, foreach, methods, rebmix, GenomicRanges, IRanges, doParallel
Imports foreach, lars, sn, DNAcopy, methods, rebmix, GenomicRanges, IRanges
Suggests
System Requirements
URL
Depends On Me
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Package Downloads

Package Source SomatiCA_1.7.0.tar.gz
Windows Binary SomatiCA_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SomatiCA_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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