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