The following repository contains all of the code and datasets used for the project "Understanding Selective Pressures throughout Cancer Evolution". This project was completed to fufil the requirements for the BHSc honours program at the University of Calgary.
CBaSE Analysis
- Assembly of MAF files into CBaSE format
- CBaSE code (Weghorn et al.) available at: http://genetics.bwh.harvard.edu/cbase/
COSMIC Analysis
- Removal of oncogenes from COSMIC db
- COSMIC hits for SKCM variants
GO Analysis
- Files used as input for Gene Ontology
- Gene Ontology Analysis conducted on DAVID: https://david.ncifcrf.gov/tools.jsp
- Output files for Gene Ontology
Mutation Analysis
- Getting lengths of genes (Ensemble Biomart)
- Normalize gene mutation counts with gene lengths