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 following open-source projects directly incorporate components of the crisprVerse ecosystem:

• CRISPRware — Context-aware gRNA library design platform.
• CRISPR-BEasy — Web platform for designing sgRNA tiling libraries for CRISPR base-editing screens.
• PrEditR — Analysis framework for prime-editing experiments.
• crisprCHOPOFF — R wrapper for CHOPOFF, a CRISPR OFF target search algorithm
• HemTools — A collection of NGS pipelines and bioinformatic analyses
• Digenome Detect — Digenome-seq analysis tool
• snakemake-crispr-guides — Guide design workflow developed by the Max Planck Unit for the Science of Pathogens.

• Template-driven scaffolding of SCF-FBXO42 regulates PP2A degradation (Nature)
• Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView (Nature Biotechnology)
• Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations (Nature Biotechnology)
• Microglia-mediated protection against Alzheimer's disease pathology and detrimental effects in white matter revealed by Ptpn6 deletion (Neuron)
• Rational design of potent small-molecule SMARCA2/A4 degraders acting via the recruitment of FBXO22 (Nature Communications)
• A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular anti-sense oligonucleotide activity (Nature Communications)
• Inhibition of GPX4 enhances CDK4/6 inhibitor and endocrine therapy activity in breast cancer (Nature Communications)
• Advancing the genetic engineering toolbox by combining AsCas12a knock-in mice with ultra-compact screening (Nature Communications)
• Accelerated drug-resistant variant discovery with an enhanced, scalable mutagenic base editor platform (Cell Reports)
• CRISPR activation screens identify the SWI/SNF ATPases as suppressors of ferroptosis (Cell Reports)
• Seed sequences mediate off-target activity in the CRISPR-interference system (Cell Genomics)
• An unbiased whole-genome open reading frame overexpression screen identifies B3GALT2, a novel inducer of cellular ASO activity (Molecular Therapy Nucleid Acids)
• Scalable multimodal mapping of macrophage regulatory architecture by integrating optical and transcriptomic pooled screens (bioRxiv)
• A novel, high-density CRISPR activation platform for mapping cancer dependencies and resistance pathways ex vivo and in vivo (bioRxiv)

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.