To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TitanCNA")

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

TitanCNA

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see TitanCNA.

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Bioconductor version: 3.1

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data.

Author: Gavin Ha, Sohrab P Shah

Maintainer: Gavin Ha <gavinha at gmail.com>, Sohrab P Shah <sshah at bccrc.ca>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TitanCNA")

Documentation

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

browseVignettes("TitanCNA")
PDF R Script TitanCNA
PDF Reference Manual
Text README
Text LICENSE

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, Sequencing, Software, StatisticalMethod, WholeGenome
Version 1.6.0
In Bioconductor since BioC 2.14 (R-3.1) (2 years)
License file LICENSE
Depends R (>= 3.1.0), foreach (>= 1.4.0), IRanges(>= 1.99.1), Rsamtools(>= 1.17.11), GenomeInfoDb(>= 1.1.3)
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL https://github.com/gavinha/TitanCNA
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source TitanCNA_1.6.0.tar.gz
Windows Binary TitanCNA_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) TitanCNA_1.6.0.tgz
Mac OS X 10.9 (Mavericks) TitanCNA_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/TitanCNA/tree/release-3.1
Package Short Url http://bioconductor.org/packages/TitanCNA/
Package Downloads Report Download Stats

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