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

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

TitanCNA.pdf PDF R Script
Reference Manual PDF


biocViews CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, Software, StatisticalMethod, WholeGenome
Version 1.42.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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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Follow Installation instructions to use this package in your R session.

Source Package TitanCNA_1.42.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) TitanCNA_1.42.0.tgz
macOS Binary (arm64) TitanCNA_1.42.0.tgz
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Source Repository (Developer Access) git clone
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