# Crisprviz

> crisprViz

- Skill: `biomate-ai/crisprviz` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biomate-ai/crisprviz`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biomate-ai/crisprviz/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: biomate-ai (https://skillmd.com/u/biomate-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biomate-ai/crisprviz

---


# 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.

## When NOT to Use
- **Unsupported R/Bioconductor Versions**: Do not use if R version is less than 4.2.0 or Bioconductor version is less than 3.16.
- **gRNA Design or Scoring**: Do not use for designing gRNAs or calculating scores directly (use `crisprDesign` and `crisprScore` instead).

## Data Requirements
- **GuideSet**: A `GuideSet` object containing candidate gRNAs (e.g., `krasGuideSet`).
- **Gene Model**: A gene model represented as a `GRangesList` object (e.g., `krasGeneModel`).
- **Reference Genome**: A `BSgenome` object for genomic sequence visualization (e.g., `BSgenome.Hsapiens.UCSC.hg38`).

## Key Parameters
- **geneModel** (no default): A `GRangesList` object describing the gene structure.
- **targetGene** (no default): Character string specifying the name of the target gene.
- **from** (NULL): Numeric coordinate specifying the start of the plot window.
- **to** (NULL): Numeric coordinate specifying the end of the plot window.
- **extend.left** (0): Numeric value to extend the plot window to the left.
- **extend.right** (0): Numeric value to extend the plot window to the right.
- **showGuideLabels** (TRUE): Logical indicating whether to display gRNA labels.
- **pamSiteOnly** (FALSE): Logical indicating whether to plot only the PAM site instead of the full protospacer.
- **onTargetScore** (NULL): Character string specifying the metadata column name containing on-target scores.
- **annotations** (NULL): Named list of `GRanges` objects representing genomic annotations.
- **gcWindow** (NULL): Integer specifying the window size for calculating percent GC content.

## Best Practices
- **Window Adjustment**: Adjust the plot window manually using `from`, `to`, `extend.left`, and `extend.right` to show the entire gene or focus on a specific exon.
- **Crowding Prevention**: Set `showGuideLabels = FALSE` when plotting a large number of candidate gRNAs to avoid crowding the plot space.
- **PAM Site Only**: Set `pamSiteOnly = TRUE` when visualizing many overlapping gRNAs in a small window to simplify the plot.
- **Pre-filtering**: Filter out gRNAs overlapping repeat elements or SNPs using `crisprDesign::removeRepeats` before plotting to ensure high-quality selections.

## Common Pitfalls
- **Rendering Errors**: Plotting too many gene isoforms or gRNAs in a small graphical device, resulting in rendering errors. Fix: Increase the height/width of the plot space using `grDevices::quartz` or similar device settings.

## Alternatives
- **Gviz**: For general genomic track visualization (which `crisprViz` is built upon).
- **biovizBase**: For nucleotide color schemes and basic genomic plotting utilities.

## Citations
- No specific primary publication is cited in the vignette text, but the package is part of the `crisprVerse` ecosystem.

## References
- Homepage: bioconductor.org/packages/crisprViz
- Vignette: bioconductor.org/packages/release/bioc/vignettes/crisprViz/inst/doc/introduction.html