SimCopy

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Title SimCopy
Short Description An R package simulating the evolution of copy number profiles along a tree.
Long Description SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them. Please note, that the SimCopy simulations are restricted to a single chromosome. The genomes are encoded as a sequence of sites containing integers identifying genomic regions. Negative integers represent inverted genomic regions. SimCopy supports 1) deletion - deletes genomic regions, 2) duplication - duplicates genomic regions, 3) inversion - changes the orientation of the genomic regions by taking the opposite of the corresponding integer, 4) inverted duplication - duplicates genomic regions and flips their orientation and 5) translocation - translocates a stretch of genomic regions.
Version 0.2
Project Started 2012
Last Release 5 years, 11 months ago
Homepagehttp://bit.ly/simcopy
Citations Roland F. Schwarz, Anne Trinh, Botond Sipos, James D. Brenton, Nick Goldman, and Florian Markowetz , Phylogenetic Quantification of Intra-tumour Heterogeneity, PLoS Comput Biol, April 10, 2014
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