TitanCNA

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see TitanCNA.

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


Bioconductor version: 3.7

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

Author: Gavin Ha, Sohrab P Shah

Maintainer: Gavin Ha <gavinha at broadinstitute.org>, Sohrab P Shah <sshah at bccrc.ca>

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

Installation

To install this package, start R (version "3.5") 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

Details

biocViews CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, Sequencing, Software, StatisticalMethod, WholeGenome
Version 1.18.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-3
Depends R (>= 3.3.2)
Imports IRanges(>= 2.6.1), GenomicRanges(>= 1.24.3), VariantAnnotation(>= 1.18.7), foreach (>= 1.4.3), Rsamtools(>= 1.24.0), 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.

Source Package TitanCNA_1.18.0.tar.gz
Windows Binary TitanCNA_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) TitanCNA_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TitanCNA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TitanCNA
Package Short Url https://bioconductor.org/packages/TitanCNA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive