Programmable genome editing using CRISPR has tremendously advanced life sciences. To facilitate the use of this technology, especially in the noncoding genome and for batch screens, we developed GuideScan, a fully customizable CRISPR guide RNA (gRNA) design tool. We recently developed GuideScan2 with substantially expanded and new functionality for memory-efficient, parallelizable construction of high-specificity gRNA databases and user-friendly gRNA design in custom genomes. We now continue working on tools for design and analysis of CRISPR-based genome perturbations and their combinations with single-cell functional genomic assays.