QuantumClone: Clustering Mutations using High Throughput Sequencing (HTS) Data

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. Latest version can be found at github/DeveauP/QuantumClone .

Version: 0.15.11
Depends: R (≥ 3.1.0), fpc, foreach
Imports: doParallel, parallel, gridExtra, rgl
Suggests: ggplot2, knitr, rmarkdown
Published: 2015-11-03
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau at curie.fr>
License: GPL-2
NeedsCompilation: no
Materials: README
CRAN checks: QuantumClone results

Downloads:

Reference manual: QuantumClone.pdf
Vignettes: Release
Use case
Package source: QuantumClone_0.15.11.tar.gz
Windows binaries: r-devel: QuantumClone_0.15.11.zip, r-release: QuantumClone_0.15.11.zip, r-oldrel: QuantumClone_0.15.11.zip
OS X Snow Leopard binaries: r-release: QuantumClone_0.6.15.tgz, r-oldrel: not available
OS X Mavericks binaries: r-release: QuantumClone_0.15.11.tgz
Old sources: QuantumClone archive