TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Bioconductor version: Release (3.20)
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 "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, DNASeq, ExomeSeq, Genetics, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, Software, StatisticalMethod, WholeGenome |
| Version | 1.44.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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) |
| 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_1.44.0.tar.gz |
| Windows Binary (x86_64) | TitanCNA_1.44.0.zip |
| macOS Binary (x86_64) | TitanCNA_1.44.0.tgz |
| macOS Binary (arm64) | TitanCNA_1.43.0.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 |