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The CloneFinder R-Forge project is one component of the broader OOMPA Project produced by the Coombes Lab over the past decade. it consists of a set of packages to understand genetic structural variations and how the evolution of tumors gives rise to distinct clones.


Support for all packages that are part of the OOMPA family uses a common set of discussion forums and bug trackers:

List of Packages

The CloneSeeker package was developed as part of Mark Zucker's PhD thesis, and its description can be found in the paper by Zucker and colleagues. The method uses bulk cytogenetic data (arising, for example, from the analysis of SNP-chip or comparative genomic hybridization data) to reconstruct the clonal architecture of a specific tumor. It can also use mutation allele frequency data (with or without the cytogentic structural variaiton data) for the same purpose.
CloneData is a data package, containing the data that was simulated to support Mark Zucker's PhD thesis and his paper in Bioinformatics. It also includes the code to generate those simulations.
The SVAlignR package is still under development, which is why it has not yet been submitted to CRAN. The goal is to study long-read sequences (such as those from Oxford Nanopore or Pacific Biosystems) from virus-associated tumors in order to determine if the virus is actually incorporated into the host genome or if it merely exists as extrachromosomal units that possibly include copies of pieces of the host genome.

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