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TitanCNA

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, Software, StatisticalMethod, WholeGenome
Version 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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)
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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_1.38.0.tar.gz
Windows Binary TitanCNA_1.38.0.zip
macOS Binary (x86_64) TitanCNA_1.38.0.tgz
macOS Binary (arm64) TitanCNA_1.38.0.tgz
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/
Package Downloads Report Download Stats