/ctree

Clone trees for Cancer Evolution studies from bulk sequencing data.

Primary LanguageR

ctree

R-CMD-check

pkgdown

Lifecycle: stable

Thee ctree package provides a simple implementation of clones trees in cancer.

clone trees that can be build of Cancer Cell Franctions (CCFs) clusters computed by tumour subclonal deconvolution. This type of models can be used to study the evolutionary trajectories of a tumour from bulk sequencing data.

Clone trees can be built from Cancer Cell Franctions (CCFs) data reporting fraction of cancer cells harbouring a somatic mutation (usually, a single-nucleotide variant) across a number of tumour regions. This type of models can be used to study the evolutionary trajectories of a tumour from bulk sequencing data, especially in setups where one can generate whole-genome sequencing data.

  • ctree provides an S3-based implementation of mutation trees, as well as a Monte Carlo sampler that has been discussed in Caravagna et al; PMID: 30171232. The package provides also functions to plot and analyze the trees.

  • The sibling of a clone tree is a mutation tree, which is obtained from the analysis of binary absence/ presence profiles of somatic variants from bulk targeted panels; mutation trees are implemented in the mtree package.

ctree is part of the evoverse, a set of R packages to implement Cancer Evolution analyses.

Help and support

Installation

You can install the released version of ctree from GitHub with:

# install.packages("devtools")
devtools::install_github("caravagn/ctree")

Copyright and contacts

Giulio Caravagna, PhD. Institute of Cancer Research, London, UK.