This repository contains Rmd scripts relevant to the downstream analysis of CRISPRtOE data. It also contains the input files required to run these analyses, which came from running the ctoe_analysis pipeline.
The first step in the downstream analysis is to run edgeR. Relevant Rmd files can be found in the edgeR directory. edgeR version 4.4.2 was used.
Briefly, raw count data are filtered to a minimum CPM in at least half of samples being used to build edgeR models and normalization factors are calculated with the trimmed mean of M-values method.
The modeling framework used is the negative binomial GLM, fit with a quasi-likelihood method using the robust dispersion estimation. Modeling is set up fo ascertain the effects of library type and treatment type independently, as well as the library * treatment interaction.
Insertion-level data are combined into a gene-level analysis using CAMERA.
The edgeR scripts produce output files that are used in the other analysis scripts, such as those used to build bar plots for individual genes, and those for correlating CPM and log2FC values between replicates and/or library types.