modules/ctree
Clone trees for Cancer Evolution studies from bulk sequencing data.
Output
The output varies based on the input. If the input is an object of class dbpmm,
the module outputs one object per sample as follows: SampleID/ctree_mobster.rds.
If the input is an object of class vb_bmm, the output will be one ctree object
named ctree_VIBER.rds. If the input is the pyclonevi .tsv file, the output will
be one ctree object named ctree_pyclonevi.rds
**ctree_{mobster,VIBER,pyclonevi}.rdsTools
ctree GPL v3-or-later
The ctree package implements clones trees for cancer evolutionary studies. These models are built from Cancer Cell Franctions (CCFs) clusters computed via tumour subclonal deconvolution, using either one or more tumour biopsies at once. They can be used to model evolutionary trajectories from bulk sequencing data, especially if whole-genome sequencing is available.
