Fig. 2

Unsupervised detection of segments of equal sgRNA logFCs and their correction. a and b Example segments of equal gene copy number and equal sgRNA logFC values detected and corrected by CRISPRcleanR in two cell lines. c logFC values of sgRNAs of the entire library for all cell lines grouped according to the copy number of their targeted gene before (left) and after (right) CRISPRcleanR correction. Box-plots show the median, inter-quartile ranges and 95% confidence intervals. d Recall curves of sgRNA when classified as targeting amplified genes, amplified non-expressed genes, FE genes, and non-essential genes before and after CRISPRcleanR correction, for an example cell line (EPLC−272H). e Assessment of CRISPRcleanR correction comparing Recall at 5% FDR (top row) or area under the Recall curve (AURC, bottom row) of genes in six predefined gene sets based on their uncorrected or corrected logFCs (averaged across targeting sgRNAs)