Package for investigating complex copy number changes and structural variants
Dependencies: parallel, GenomicRanges
Implements three of the tests for chromothripsis from Korbel & Campbell (2013). Tests for departure from exponentially distributed distances between breakpoints, equal proportion of HH, HT, TH and TT fusions partners, and random choice of fusion partners.
Implements tests for genome doubling from Dewhurst et al. (2013) and Carter et al. (2012).
Implements copy number scoring from Davoli et al. (2017).
Implements identification of rearrangement signatures as described in Nik-Zainal et al. (2016).
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