chymera-scoring

This repository contains all scripts used to score data from the paper "Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform", available to read at https://crispr.ccbr.utoronto.ca/chymera/index.html.

To run the script "score_paralogs.R" and generate scores for the paralog CHyMErA library, perform the following steps:

1. Make sure that you have R version > 3.6.3 installed, along with the packages ggplot2 and ggthemes.
2. Change the four parameters at the top of the script to match your local machine.
   1. setwd takes the path of the chymera-scoring folder.
   2. output_folder is the path to a desired output folder. This will be created automatically if it does not exist.
   3. which_cell_line is one of "hap1", "rpe1", or "hap1_torin" for scoring each screen, respectively.
3. Run the script, e.g. with source("score_paralogs.R"), to score the type of data specified in step 2.3.

To run the script "score_dual_targeting.R" and generate scores for the dual-targeting CHyMErA libraries, perform the following steps:

1. Make sure that you have R version > 3.6.3 installed, along with the packages ggplot2 and ggthemes.
2. Change the four parameters at the top of the script to match your local machine.
   1. setwd takes the path of the chymera-scoring folder.
   2. output_folder is the path to a desired output folder. This will be created automatically if it does not exist.
   3. guide_type is one of "single", "dual", "paralog_single" or "paralog_dual" for scoring single-targeting guides or dual-targeting guides from the dual-targeting library ("single" and "dual") or the paralog library ("paralog_single" and "paralog_dual").
3. Run the script, e.g. with source("score_dual_targeting.R"), to score the type of data specified in step 2.3.

To run the script "score_exon.R" and generate scores for the exon deletion CHyMErA library, perform the following steps:

1. Make sure that you have R version > 3.6.3 installed, along with the packages ggplot2, ggthemes, dplyr and scales.
2. Change the two parameters at the top of the script to match your local machine.
   1. setwd takes the path of the chymera-scoring folder.
   2. output_folder is the path to a desired output folder. This will be created automatically if it does not exist.
3. Run the script, e.g. with source("score_exon.R").