crisprViz

Workflows

Standard Workflow

library(crisprViz)
library(BSgenome.Hsapiens.UCSC.hg38)
data("krasGuideSet", package="crisprViz")
data("krasGeneModel", package="crisprViz")

plotGuideSet(krasGuideSet[1:4], geneModel=krasGeneModel, targetGene="KRAS")

Inputs: A GuideSet object (krasGuideSet) and a gene model GRangesList (krasGeneModel). Outputs: A genomic track plot visualizing the gRNAs against the gene model.

Compare Multiple Guidesets

library(crisprViz)
library(BSgenome.Hsapiens.UCSC.hg38)
data("cas9GuideSet", package="crisprViz")
data("cas12aGuideSet", package="crisprViz")
data("ltn1GeneModel", package="crisprViz")

plotMultipleGuideSets(list(SpCas9=cas9GuideSet, AsCas12a=cas12aGuideSet),
                      geneModel=ltn1GeneModel,
                      targetGene="LTN1",
                      bsgenome=BSgenome.Hsapiens.UCSC.hg38,
                      margin=0.2,
                      gcWindow=10)

Inputs: A list of GuideSet objects for different nucleases, a gene model, and a reference BSgenome object. Outputs: A multi-track genomic plot comparing target distributions and GC content.

When to Use

• gRNA Track Visualization: Visualizing gRNA cutting locations against target genes or genomic regions using plotGuideSet.
• Nuclease Comparison: Comparing multiple GuideSet objects targeting the same region side-by-side using plotMultipleGuideSets.
• Genomic Annotations: Adding genomic annotations (e.g., repeat elements, CAGE peaks, DNase I hypersensitivity sites) to gRNA plots using the annotations argument.
• Score-Based Color Coding: Coloring gRNAs based on on-target efficiency scores (e.g., DeepHF) using the onTargetScore argument.