Genetic screens by CRISPR/Cas9-mediated genome engineering have become a powerful tool for functional genomics. However, there is currently a lack of end-to-end software pipelines to analyze CRISPR/Cas9 screens based on next generation sequencing. Source text: Winter et al., 2015.
CRISPR-AnalyzeR for pooled screens
CRISPR-AnalyzeR for pooled screens
caRpools
An R package for exploratory data analysis that provides a complete workflow to analyze…
An R package for exploratory data analysis that provides a complete workflow to analyze CRISPR/Cas9 screens. To further support the analysis of large-scale screens, caRpools integrates screening documentation and generation of standardized analysis…
HiTSelect
HiTSelect
A comprehensive analysis pipeline for rigorously selecting screen hits and identifying…
A comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of…
Model-based Analysis of Genome-wide CRISPR/Cas9…
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout
MAGeCK
Identifies positively and negatively selected sgRNAs and genes in genome-scale…
Identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. It consists of four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. MAGeCK outperforms existing…
Screening Bayesian Evaluation and Analysis Method
Screening Bayesian Evaluation and Analysis Method
ScreenBEAM
A hierarchical modelling algorithm within Bayesian framework for meta-analysis of…
A hierarchical modelling algorithm within Bayesian framework for meta-analysis of large-scale FG screens. This novel multi-probe approach performs more robustly than previously established analysis methods, especially with noisy high-throughput…