Bioconductor – Clomial

DOI: 10.18129/B9.bioc.Clomial  

 

This package is for version 3.12 of Bioconductor;
for the stable, up-to-date release version, see
Clomial.

Infers clonal composition of a tumor

Bioconductor version: 3.12

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
“4.0”) 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 1.26.0
In Bioconductor since BioC 2.14 (R-3.1) (7 years)
License GPL (>= 2)
Depends R (>= 2.10), matrixStats
Imports methods, permute
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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


Read more here: Source link