The crisprVerse is a Bioconductor ecosystem of R packages that enables efficient gRNA design and annotation for a multitude of CRISPR technologies, including CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe), and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a comprehensive, user-friendly, and unified interface to add on- and off-target annotations via several alignment methods, rich gene and SNP annotations, and a dozen on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, Cas13, and Csm. Both single and paired gRNA designs are enabled.

For an overview of the ecosystem functionalities, see the crisprDesign page. For detailed examples, see our tutorials.

• Project lead: Jean-Philippe Fortin
• Maintainers: Luke Hoberecht, Jean-Philippe Fortin
• Contributors: Aaron Lun, Pirunthan Perampalam

The crisprVerse is supported for macOS, Linux and Windows machines. It requires R version >=4.4. Some of the third-party functionalities are not available for Windows machines (BWA alignment, and some of the scoring functions). To download and install R, see the R-project website.

The crisprVerse is embedded within the Bioconductor ecosystem, therefore has 2 concurrent branches: release and devel. Currently (July 2024), the release branch is 3.19, and the devel branch is 3.20. Both branches requires R version 4.4 or higher. Release versions are created twice a year. See the Bioconductor install page for more information regarding Bioconductor versions and to get an overview of how to install packages.

To install the packages from the release branch, type in the following commands in an R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version="release") 
BiocManager::install("crisprVerse")

To install the packages from the development branch, which is up to date with the lastest pushes to the GitHub repos, type in the following commands in an R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version="devel") 
BiocManager::install("crisprVerse")

The optional data package crisprDesignData can be installed from GitHub using the following commands:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
    
devtools::install_github("crisprVerse/crisprDesignData")

For maxOS and Linux users, the crisprBwa can be installed from Bioconductor using the following:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crisprBwa")

We are providing ready-to-use Docker images that can be downloaded from the Docker hub. See our Docker page for more information.

A comprehensive list of tutorials can be found here. Tutorials are often updated to take into account the latest functionalities and changes of the ecosystem.

Package	BioC-release	BioC-devel	Description
crisprVerse			Easily install of the crisprVerse ecosystem
crisprDesign			Core gRNA design package across nucleases and applications
crisprBase			Base functions and classes for CRISPR gRNA design
crisprBowtie			Alignment of gRNA spacer sequences using bowtie
crisprBwa			Alignment of gRNA spacer sequences using BWA
crisprScore			On-target and off-target scoring for CRISPR gRNAs
crisprScoreData			Pre-trained models for the crisprScore package
crisprViz			Visualization of CRISPR gRNAs using genomic tracks
crisprShiny			Shiny interface for CRISPR gRNAs
screenCounter			gRNA barcode sequencing reads alignment tool
Rbwa			R wrapper for BWA-backtrack and BWA-MEM aligners

Package	Devel	Description
crisprDesignData		Useful data for the crisprVerse ecosystem

If using our software, please cite our Nature Communications paper A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Here's a bibtex citation:

@article{hoberecht2022comprehensive,
  title={A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies},
  author={Hoberecht, Luke and Perampalam, Pirunthan and Lun, Aaron and Fortin, Jean-Philippe},
  journal={Nature Communications},
  volume={13},
  number={1},
  pages={6568},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

The ecosystem is released under the MIT license. Genentech Inc. owns the copyright.