OOMPA Overview

OOMPA PROJECT

CloneFinder

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.

List of Packages

CloneSeeker

Seeking and Finding Clones in Copy Number and Sequencing Data 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 variation data) for the same purpose.

CloneData

Data to Support CloneSeeker Algorithm 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.

SVAlignR

Recovering Structure of Long Molecules from Structural Variation Data 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.