bioconductor-crisprdesign

name

bioconductor-crisprdesign

description

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

crisprDesign

Workflows

Standard Workflow

library(crisprDesign)
library(BSgenome.Hsapiens.UCSC.hg38)
data(grListExample, package="crisprDesign")
data(BE4max, package="crisprBase")

bsgenome <- BSgenome.Hsapiens.UCSC.hg38
gr <- queryTxObject(txObject=grListExample, featureType="cds", queryColumn="gene_symbol", queryValue="IQSEC3")
gr  gr

guideSet  findSpacersgr bsgenomebsgenome crisprNucleaseBE4max strict_overlap