Comparing the predictors of mutability among healthy human tissues inferred from mutations in single cell genome data

by Madeleine Oman and Rob W Ness

This is the repository that contains all the analyses and code used in the above publication. Snakemake was used as a project manager, and the workflow can be visualized in the following documents:

• rulegraph.pdf : the basic bones of the whole analysis, from the webscraping all the way to figure generation
• dag.pdf : the whole workflow. basically the "rulegraph" workflow but for every tissue
• filegraph.pdf : the workflow but with the linking files explicitely given between steps.

the "Snakefile" file dictates the wrokflow, and contains all the rules and requirements explicitely.

To run the analyses with Snakemake, first install it in your shell:

conda install -n mutability -c conda-forge mambareplacing "mutability" with the environment you are working from.

mamba create -c conda-forge -c bioconda -n snakemake snakemake to set up the mamba environment in which to run

Beyond this, all packages required for the analyses are managed by snakemake, listed explictly in the .yml files here.

Reach out if you have any questions! [email protected]