crisprScore

crisprScore provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs).

Key Features:

• Multi-nuclease support: Supports SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx) nucleases.
• On-target cutting efficiency scoring: Implements RuleSet1, RuleSet3, DeepHF, enPAM+GB, and CRISPRscan scoring methods.
• Off-target specificity prediction: Provides CFD and MIT scoring methods for off-target prediction.
• Frameshift prediction: Provides a Lindel-derived score to predict the probability of a gRNA producing indels that induce a frameshift for the Cas9 nuclease.
• Platform limitation: DeepHF and enPAM+GB are not available on Windows machines.

Scientific Applications:

• CRISPR gRNA design optimization: Scores gRNAs for on-target cutting efficiency across multiple nuclease systems.
• Off-target risk assessment: Predicts off-target specificity to minimize unintended genome editing.
• Frameshift outcome prediction: Predicts the likelihood of generating frameshift-inducing indels for gene knockout applications with Cas9.

Methodology:

The package provides R wrappers for established scoring algorithms; specific computational steps for each scoring method are implemented as wrapped functions calling the underlying algorithms.