R scripts utilised for the analysis of Tasmanian devil genomic analyses used in our study "The origins and vulnerabilities of two transmissible cancers in Tasmanian devils". Cancer Cell 33(4), 607-619 (2018).
- Genomic data (BAM files) can be accessed via the European Nucleotide Archive: https://www.ebi.ac.uk/ena/data/view/PRJEB21902
- Additional tables, FISH, genome assembly, IHC and mutation data is available via Mendeley data: http://dx.doi.org/10.17632/znfphvhmbv.1
- integrate and process SNP data from 398 Tasmanian devils by Brüniche-Olsen et al., 2016
- integrate genotype calls of our samples
- 86T, 88T (DFT1)
- 202T2, 203T3 (DFT2)
- 91H, 202H1, 203H (Normals)
- draw hierarchical clustering map
- integrate somatic DFT1 and DFT2 single-nucleotide variants (SNVs)
- draw somatic mutational spectrum of DFT1 (86T-unique & 88T-unique)
- draw somatic mutational spectrum of DFT2 (202T2-unique & 203T3-unique)
- normalise 30 COSMIC signatures to Tasmanian devil 7.1 reference genome base-triplet frequency
- fit DFT1 and DFT2 mutational spectrum to different combinations of COSMIC signatures
- integrate DFT1 and DFT2 structural variant (SV) calls
- draw circos plots by sample
- draw barplots of SV repair classes by sample
- integrate copy-number calls
- integrate gene dosage alteration calls
- draw Venn diagrams
- draw PDGFRA, PDGFRB and B2M Campbellgrams
- integrate drug screening IC50 data from DFT1, DFT2 and human cancer cell lines (https://www.cancerrxgene.org/, Yang et al., 2014)
- process samples
- draw hierarchical clustering map
- draw cross-sample IC50 boxplots with sample-wise 'beeswarming', for drugs Afatinib, Axitinib, Sorafenib, Dasatinib, Talazoparib and AZD7762