To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

SomatiCA

 

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

Bioconductor version: Release (3.1)

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>

Citation (from within R, enter citation("SomatiCA")):

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

Details

biocViews CopyNumberVariation, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 2.12 (R-3.0) (2 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
LinkingTo
Suggests
SystemRequirements
Enhances sn, SomatiCAData
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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Package Source SomatiCA_1.12.0.tar.gz
Windows Binary SomatiCA_1.12.0.zip
Mac OS X 10.6 (Snow Leopard) SomatiCA_1.12.0.tgz
Mac OS X 10.9 (Mavericks) SomatiCA_1.12.0.tgz
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