Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
This repository contains code corresponding to analysis reported in Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
The submodules in this repository link to the version of the code that was used to produce the results and are provided as a permanent archive.
Some of the methods may see further development, therefore, if you're interested in applying a method it is encouraged to go to the linked repositories and check out the latest version there.
Data from the Pan-Cancer Analysis of Whole Genomes project (PCAWG) is available here, including consensus copy number profiles and consensus subclonal architectures.
| Repository | Description |
|---|---|
| CICC | Method to construct a consensus subclonal architecture |
| CSR | Method to construct a consensus subclonal architecture |
| SimClone1000 | Pipeline that created the SimClone1000 simulated data set |
| icgc_consensus_copynumber | Pipeline that constructs the consensus copy number profiles |
| icgc_consensus_purity | Pipeline that establishes a consensus purity estimate |
| icgc_consensus_clustering_assignment | Pipeline that assigns all SNVs, indels and SVs to consensus mutation clusters |
| MutationTimeR | Version of MutationTimeR used to assign mutations to clusters |
| weme | Method to construct a consensus subclonal architecture |
| SpoilSport | Method to correct cluster positions and sizes for missed SNVs (i.e. winner's curse) |
Each of the above named repositories contains a description of the depencies required for that component.
- ABSOLUTE - code - paper
- Aceseq - code - paper
- Battenberg - code - paper
- cloneHD - code - paper
- JaBbA - code - paper
- Sclust - code - paper