mobster

mobster is a package that implements a model-based approach for subclonal deconvolution of cancer genome sequencing data (Caravagna et al; PMID: 32879509).

The package integrates evolutionary theory (i.e., population) and Machine-Learning to analyze (e.g., whole-genome) bulk data from cancer samples. This analysis relates to clustering; we approach it via a maximum-likelihood formulation of Dirichlet mixture models, and use bootstrap routines to assess the confidence of the parameters. The package implements S3 objects to visualize the data and the fits.

mobster is part of the evoverse set of R packages to implement Cancer Evolution analyses.

Citation

If you use mobster, please cite:

  • G. Caravagna, T. Heide, M.J. Williams, L. Zapata, D. Nichol, K. Chkhaidze, W. Cross, G.D. Cresswell, B. Werner, A. Acar, L. Chesler, C.P. Barnes, G. Sanguinetti, T.A. Graham, A. Sottoriva. Subclonal reconstruction of tumors by using machine learning and population genetics. Nature Genetics 52, 898–907 (2020).

Help and support

Installation

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

# install.packages("devtools")
devtools::install_github("caravagnalab/mobster")