CRISPR interference (CRISPRi) and activation (CRISPRa) are powerful tools for targeted gene regulation, enabling high-resolution functional genomics studies. However, designing effective guide RNA (gRNA) libraries for these applications requires careful consideration of genomic context and guide spacing. This process requires programming experience and is time consuming, meaning it is often inaccessible to many biologists.
We have developed an interactive Shiny application that simplifies the design of CRISPRi/a guide RNAs for non-computational biologists. The tool integrates sequence extraction from user-defined genomic regions, guide design via FlashFry, and selection of high-scoring guides based on optimal spacing and positioning. By automating this workflow within a user-friendly interface, the app empowers a broader community of researchers to design robust gRNA libraries for gene perturbation experiments, thereby increasing accessibility and reproducibility in CRISPR-based functional genomics.