Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing.

Documentation

Manual: QuantumClone.pdf
Vignettes:

Maintainer: Paul Deveau <paul.deveau at curie.fr>

Author(s): Paul Deveau*

Install package and any missing dependencies by running this line in your R console:

install.packages("QuantumClone")

Depends R (>= 3.1.0), compiler, foreach
Imports doParallel, parallel, gridExtra, ggplot2, NbClust, DEoptim, optimx, fpc
Suggests knitr, rmarkdown, testthat
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Package QuantumClone
Materials
URL https://github.com/DeveauP/QuantumClone
Task Views
Version 1.0.0.4
Published 2017-03-08
License GPL-2
BugReports https://github.com/DeveauP/QuantumClone/issues
SystemRequirements
NeedsCompilation no
Citation
CRAN checks QuantumClone check results
Package source QuantumClone_1.0.0.4.tar.gz