TitanCNA

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TitanCNA.

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

DOI: 10.18129/B9.bioc.TitanCNA

Bioconductor version: 3.21

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

Author: Gavin Ha

Maintainer: Gavin Ha <gha at fredhutch.org>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

TitanCNA.pdf PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, Software, StatisticalMethod, WholeGenome

Version 1.45.0

In Bioconductor since BioC 2.14 (R-3.1) (11.5 years)

License GPL-3

Depends R (>= 3.5.1)

Imports BiocGenerics(>= 0.31.6), IRanges(>= 2.6.1), GenomicRanges(>= 1.24.3), VariantAnnotation(>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb(>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0)

System Requirements

URL https://github.com/gavinha/TitanCNA

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Package Archives

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

Source Package TitanCNA_1.45.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/TitanCNA

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TitanCNA

Bioc Package Browser https://code.bioconductor.org/browse/TitanCNA/

Package Short Url https://bioconductor.org/packages/TitanCNA/

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