To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("SomatiCA")
In most cases, you don't need to download the package archive at all.
![]() ![]() |
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see SomatiCA.
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>
Citation (from within R,
enter citation("SomatiCA")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("SomatiCA")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SomatiCA")
R Script | SomatiCA Vignette | |
SomatiCAUserGuide.pdf | ||
Reference Manual | ||
Text | NEWS |
biocViews | Bioinformatics, CopyNumberVariants, Sequencing, Software |
Version | 1.4.0 |
In Bioconductor since | BioC 2.12 (R-3.0) (3 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 |
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 |
Mac OS X 10.6 (Snow Leopard) | SomatiCA_1.4.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/SomatiCA/tree/release-2.13 |
Package Short Url | http://bioconductor.org/packages/SomatiCA/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: