requirements.txt
to set up a conda environment with the relevant packages.$ conda create --name <env> --file requirements.txt
requirements.txt
)public-smith-sheltzer-cancer-analysis
..
) and the number of parallel workers to use for the analysis (default none, and a sequential only analysis.). With -p 4
, run.py takes ~12 hours on a 2017 MacBook Pro.$ python run.py -p 4 -o $ouput_directory
analysis.py
has the meat of cox analysismutation_base.py
has the repeatable processing required to turn raw mutation data into usable dataframes.process_copy_numbers_to_genes.py
has the repeatable processing to turn copy number raw data into usable dataframes.