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Bioconductor - TitanCNA

TitanCNA

This is the released version of TitanCNA; for the devel version, see TitanCNA.

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

Bioconductor version: Release (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")
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 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 See More Suggests Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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