Clomial

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see Clomial.

Infers clonal composition of a tumor

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, Clustering, DNASeq, ExomeSeq, GeneticVariability, Genetics, ImmunoOncology, MultipleComparison, Sequencing, Software, TargetedResequencing

Version 1.44.0

In Bioconductor since BioC 2.14 (R-3.1) (11.5 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_1.44.0.tar.gz

Windows Binary (x86_64) Clomial_1.44.0.zip (64-bit only)

macOS Binary (x86_64) Clomial_1.44.0.tgz

macOS Binary (arm64) Clomial_1.44.0.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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