Clomial

DOI: 10.18129/B9.bioc.Clomial    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see Clomial.

Infers clonal composition of a tumor

Bioconductor version: 3.11

Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

Author: Habil Zare and Alex Hu

Maintainer: Habil Zare <zare at u.washington.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Clomial")

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("Clomial")

 

PDF	R Script	A likelihood maximization approach to infer the clonal structure of a cancer using multiple tumor samples
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Clustering, DNASeq, ExomeSeq, GeneticVariability, Genetics, ImmunoOncology, MultipleComparison, Sequencing, Software, TargetedResequencing
Version	1.24.0
In Bioconductor since	BioC 2.14 (R-3.1) (6.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10), matrixStats
Imports	methods, permute
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Package Archives

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

Source Package	Clomial_1.24.0.tar.gz
Windows Binary	Clomial_1.24.0.zip
macOS 10.13 (High Sierra)	Clomial_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Clomial
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Clomial
Package Short Url	https://bioconductor.org/packages/Clomial/
Package Downloads Report	Download Stats