Correlation of profiles for CRISPR guides targeting the same gene

[gwaybio]

Here I answer the question what is the correlation across profiles generated by guides targeting the same gene.

Individual genes across cell lines

Overall density of guide correlation

Additional Points

• I update the environment.yml to include several R packages
• I also add __pycache__ to ignore
• closes [Hotfix] Analyze Audits Notebook #5
• refs BRAF1 and BRAF #6 (I might need to update these figures if BRAF1 and BRAF #6 resolves)
• I add a script that generates the audit data (see 1.analyze-audits/generate_audits.sh in aa9c1b5)
• Uses updated audit function introduced in Adding custom --null_quantile flag in audit cytominer_scripts#25
• refs What is "Chr2" in Metadata_gene_name? #2 for Chr2
  • Non-genic control that causes profiles to differ b/c of differential DNA damage induced by editing