ccube is an R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data. The method takes the reference and alternative allele read counts of called variants, corrects for copy number alterations and purity, then produces CCF estimates for all variants within the tumour sample. It identifies clusters of mutations, which can be used to determine the clonal architecture of the sample.
The package contains four Bayesian mixture models, all fitted with variational inference.
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