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

SomatiCA

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

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SomatiCA")

 

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

Details

biocViews	Bioinformatics, CopyNumberVariants, Sequencing, Software
Version	1.4.0
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
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System Requirements
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Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	SomatiCA_1.4.0.tar.gz
Windows Binary	SomatiCA_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	SomatiCA_1.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats