TitanCNA

DOI: 10.18129/B9.bioc.TitanCNA  

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

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

PDF R Script TitanCNA.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, Software, StatisticalMethod, WholeGenome
Version 1.36.0
In Bioconductor since BioC 2.14 (R-3.1) (9 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)
LinkingTo
Suggests
SystemRequirements
Enhances
URL https://github.com/gavinha/TitanCNA
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package TitanCNA_1.36.0.tar.gz
Windows Binary TitanCNA_1.36.0.zip
macOS Binary (x86_64) TitanCNA_1.36.0.tgz
macOS Binary (arm64) TitanCNA_1.36.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: