The documented code (qGI_scoring.Rmd) supports the manuscript titled "Quantitative analysis of genetic interactions in human cells from genome-wide CRISPR-Cas9 screens" (https://www.biorxiv.org/content/10.1101/2025.06.30.662330v2). It generates quantitative genetic interaction (qGI) scores from raw gRNA read counts (provided upon publication of the manuscript). This code illustrates the different data processing steps and visualizes aspects of the data where this supports a careful execution of the normalization steps. The code for additional analyses, for instance for re-scoring the data without a normalization step to judge the effect of this given normalization, is not explicitly provided here, but can be synthesized from the code. This documented code sources the qGI_functions.R source code.
The scores generated from this code are also described in the manuscript titled "A global genetic interaction map of a human cell reveals conserved principles of genetic networks" (https://www.biorxiv.org/content/10.1101/2025.06.30.662193v1).