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Clomial

Infers clonal composition of a tumor

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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")
A likelihood maximization approach to infer the clonal structure of a cancer using multiple tumor samples PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Clustering, DNASeq, ExomeSeq, GeneticVariability, Genetics, ImmunoOncology, MultipleComparison, Sequencing, Software, TargetedResequencing
Version 1.36.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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_1.36.0.tar.gz
Windows Binary Clomial_1.36.0.zip (64-bit only)
macOS Binary (x86_64) Clomial_1.36.0.tgz
macOS Binary (arm64) Clomial_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Clomial
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Clomial
Bioc Package Browser https://code.bioconductor.org/browse/Clomial/
Package Short Url https://bioconductor.org/packages/Clomial/
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