Bioconductor-mirror/SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
Version 2.3.0

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.

Getting started

Package details

AuthorMengjie Chen <[email protected]>, Hongyu Zhao <[email protected]>
Bioconductor views CopyNumberVariation Sequencing
MaintainerMengjie Chen <[email protected]>
LicenseGPL (>=2)
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor-mirror/SomatiCA documentation built on June 1, 2017, 2:23 a.m.