MAGeCKFlute - Integrative Analysis Pipeline for Pooled CRISPR Functional
Genetic Screens
CRISPR (clustered regularly interspaced short palindrome
repeats) coupled with nuclease Cas9 (CRISPR/Cas9) screens
represent a promising technology to systematically evaluate
gene functions. Data analysis for CRISPR/Cas9 screens is a
critical process that includes identifying screen hits and
exploring biological functions for these hits in downstream
analysis. We have previously developed two algorithms, MAGeCK
and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various
scenarios. These two algorithms allow users to perform quality
control, read count generation and normalization, and calculate
beta score to evaluate gene selection performance. In
downstream analysis, the biological functional analysis is
required for understanding biological functions of these
identified genes with different screening purposes. Here, We
developed MAGeCKFlute for supporting downstream analysis.
MAGeCKFlute provides several strategies to remove potential
biases within sgRNA-level read counts and gene-level beta
scores. The downstream analysis with the package includes
identifying essential, non-essential, and target-associated
genes, and performing biological functional category analysis,
pathway enrichment analysis and protein complex enrichment
analysis of these genes. The package also visualizes genes in
multiple ways to benefit users exploring screening data.
Collectively, MAGeCKFlute enables accurate identification of
essential, non-essential, and targeted genes, as well as their
related biological functions. This vignette explains the use of
the package and demonstrates typical workflows.