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>

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

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
Suggests
SystemRequirements
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URL https://github.com/gavinha/TitanCNA
Depends On Me
Imports Me
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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

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