This repository contains the code used to generate figures for the review of software tools for CRISPR-Cas.
The plots in Box 2 were generated using the Jupyter notebook entitled "box2-pdna.ipynb." We recommend you use nbviewer (https://nbviewer.jupyter.org/) to view the notebook. Simply input the github username/repository name (ruth-hanna/software-tools-review) and navigate to the notebook to view the HTML notebook.
The plots in Figure 1 were generated using the Python script entitled "annotate_clinvar_snps.py." The files entitled "summary_df_Fig1_Cas.txt" and "summary_df_Fig1_BE.txt" are the output files of annotate_clinvar_snps.py for the Cas nucleases and base editors, respectively. The "Fig1a_BE" and "Fig1a_Cas" files contain the data used to make the plot in panel a.
The figures in Figure 2, panels b-e were generated using the code in "guide-comparison.ipynb." The required input files (i.e. guide design outputs from the three tools) are included in Figure2/inputfiles.
Please contact me at rhanna [at] broadinstitute.org with any questions or comments.