Journal Club

Chaos Game Representation of Mutational Signatures (Jeya)

Signatures primer: https://en.wikipedia.org/wiki/Mutational_signatures

CGR primer: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC330698/

Review by Hannah: https://www.sciencedirect.com/science/article/pii/S2001037021004736

CGR demo: https://observablehq.com/@episphere/usm

Signatures, signatures, everywhere:

1. https://www.nature.com/articles/s41586-020-1943-3

2. https://pubmed.ncbi.nlm.nih.gov/33491650/

Forward-backward CGR: https://almob.biomedcentral.com/articles/10.1186/1748-7188-7-12

Mutational context CGRs:

1. Rust/WASM code for constructing reference genome CGRs: https://github.com/jeyabbalas/chaos-game-representation

2. Preparing ICGC Data for CGR construction: https://observablehq.com/@jeyabbalas/prepare-icgc-data-for-cgr

3. Mutational Context CGR: https://observablehq.com/@jeyabbalas/mutational-context-chaos-game-representation

Notes from presentation:

• Why there is a blank on Jeya's plot https://en.wikipedia.org/wiki/CpG_site - try to find it.

• The bitter lesson: http://www.incompleteideas.net/IncIdeas/BitterLesson.html

Hackathon

https://signal.mutationalsignatures.com