CRISPR screen analysis for TLR8 paper

Codes for the Masserumule and Passemar et al. paper.

Instructions

Install CB2 and other dependencies

install.packages("CB2")

install.packages("tidyverse")

Guide sequences

First download guide annotation from the Moffat lab website http://tko.ccbr.utoronto.ca/ for the base and the supplementary library. Then run annot2fasta.py for both the libraries to extract FASTA files.

Outputs

Start R and run source(run_cb2.R). This will produce a number of descriptive plots. guides_w_pval_fc_min.txt will have a fold change estimate per guide and an associated p-value based on the permutation test. (The results may vary across runs because of the stochastic nature of the permutation test employed.)

Citation

Maserumule, Charlotte, Charlotte Passemar, et al. 2025. “Phagosomal RNA Sensing through TLR8 Controls Susceptibility to Tuberculosis.” Cell Reports (in press).