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crisprDesign:Comprehensive design of CRISPR gRNAs for nucleases and base editors
Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.
Maintained by Jean-Philippe Fortin. Last updated 28 days ago.
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design
22 stars 8.28 score 80 scripts 3 dependentsbioc
crisprBase:Base functions and classes for CRISPR gRNA design
Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.
Maintained by Jean-Philippe Fortin. Last updated 5 months ago.
crisprfunctionalgenomicsbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequences
5 stars 7.15 score 52 scripts 6 dependents