TitanCNA

DOI: 10.18129/B9.bioc.TitanCNA    

This package is for version 3.8 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: 3.8

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 broadinstitute.org>, Sohrab P Shah <sshah at bccrc.ca>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TitanCNA")

For older versions of R, please refer to the appropriate Bioconductor release.

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
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, Software, StatisticalMethod, WholeGenome
Version	1.20.1
In Bioconductor since	BioC 2.14 (R-3.1) (5 years)
License	GPL-3
Depends	R (>= 3.3.2)
Imports	IRanges(>= 2.6.1), GenomicRanges(>= 1.24.3), VariantAnnotation(>= 1.18.7), foreach (>= 1.4.3), Rsamtools(>= 1.24.0), GenomeInfoDb(>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0)
LinkingTo
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SystemRequirements
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URL	https://github.com/gavinha/TitanCNA
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Build Report

Package Archives

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

Source Package	TitanCNA_1.20.1.tar.gz
Windows Binary	TitanCNA_1.20.1.zip
Mac OS X 10.11 (El Capitan)	TitanCNA_1.20.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TitanCNA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TitanCNA
Package Short Url	http://bioconductor.org/packages/TitanCNA/
Package Downloads Report	Download Stats