crisprBase

crisprBase provides S4 classes and CRISPR-specific genome arithmetic functions for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors to support gRNA design in downstream packages.

Key Features:

• S4 Class Infrastructure: Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.
• Genome Arithmetic Functions: Implements CRISPR-specific genome arithmetic functions to extract genomic coordinates of spacer and protospacer sequences.
• Pre-built Nuclease Objects: Supplies commonly-used CRISPR nuclease objects for immediate use in other packages.
• Dual Nuclease Support: Supports both DNA- and RNA-targeting nucleases.

Scientific Applications:

• CRISPR gRNA Design: Serves as a foundational base package enabling CRISPR guide RNA design in dependent Bioconductor packages.
• Spacer/Protospacer Coordinate Extraction: Facilitates precise genomic coordinate retrieval for spacer and protospacer sequences in CRISPR targeting applications.

Methodology:

Implements S4 object-oriented programming for nuclease classification and CRISPR-specific genome arithmetic functions for coordinate extraction.