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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see SomatiCA.

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

Bioconductor version: 3.3

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>, Hongyu Zhao <hongyu.zhao at>

Maintainer: Mengjie Chen <mengjie.chen at>

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


biocViews CopyNumberVariation, Sequencing, Software
Version 2.2.1
In Bioconductor since BioC 2.12 (R-3.0) (3.5 years)
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
Enhances sn, SomatiCAData
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