# Bioconductor Crisprviz

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on...

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-crisprviz -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-crisprviz -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-crisprviz -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-crisprviz -g -a gemini-cli -y`

## Description

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# crisprViz

## Workflows

### Standard Workflow

```r
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

```r
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.

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/transcriptomics/crisprviz/SKILL.md