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@crisprVerse

crisprVerse

Bioconductor ecosystem for CRISPR gRNA design

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Welcome to the crisprVerse, a Bioconductor ecosystem for designing CRISPR gRNAs

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, and Cas13. 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

Installation

Requirements

The crisprVerse is supported for macOS, Linux and Windows machines. It requires R version >=4.2.1 for release, and R version >=4.3 for devel. 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.

Bioconductor versions

The Bioconductor project has 2 concurrent branches: release and devel. Currently (November 2022), the release branch is 3.16, and the devel branch is 3.17. The release branch requires R version 4.2 or higher, and the devel branch requires R version 4.3 or higher. Release versions are created twice a year. See the Bioconductor install page for more information regarding Bioconductor versions.

Installing the core crisprVerse packages

Type in the following commands in an R session to install the core crisprVerse packages from the Bioconductor devel branch:

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

#BiocManager::install(version="devel") To use the devel branch instead
BiocManager::install("crisprVerse")

Optional packages

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(version="devel") To use the devel branch instead
BiocManager::install("crisprBwa")

Docker images

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

Tutorials

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.

Packages in the crisprVerse

Bioconductor packages

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

GitHub packages

Package Devel Description
crisprDesignData R-CMD-check Useful data for the crisprVerse ecosystem

Citation

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

@article{Hoberecht2022,
	author = {Hoberecht, Luke and Perampalam, Pirunthan and Lun, Aaron and Fortin, Jean-Philippe},
	title = {A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies},
	year = {2022},
	doi = {10.1101/2022.04.21.488824},
	URL = {https://www.biorxiv.org/content/early/2022/04/28/2022.04.21.488824},
	eprint = {https://www.biorxiv.org/content/early/2022/04/28/2022.04.21.488824.full.pdf},
	journal = {bioRxiv}
}

License

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

Pinned

  1. crisprVerse Public

    Collection of R packages that work in harmony for CRISPR gRNA design

    R 3

  2. Comprehensive design of CRISPR gRNAs for nucleases and base editors

    R 3

  3. crisprBase Public

    Base functions and classes for CRISPR gRNA design

    R

  4. crisprScore Public

    On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

    Python 1

  5. Useful human and mouse data for the crisprVerse ecosystem

    R

Repositories

  • .github Public
    0 MIT 0 0 0 Updated Nov 3, 2022
  • crisprVerse Public

    Collection of R packages that work in harmony for CRISPR gRNA design

    R 3 MIT 0 0 0 Updated Nov 3, 2022
  • Rbwa Public

    R wrapper for BWA-backtrack and BWA-MEM aligners

    C 0 MIT 0 0 0 Updated Nov 3, 2022
  • crisprScoreData Public

    Pre-trained models for the crisprScore package

    R 0 0 0 0 Updated Nov 3, 2022
  • crisprScore Public

    On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

    Python 1 MIT 0 4 0 Updated Nov 3, 2022
  • crisprBwa Public

    BWA-based alignment of CRISPR gRNA spacer sequences

    R 0 MIT 0 0 0 Updated Nov 3, 2022
  • crisprBowtie Public

    Bowtie-based alignment of CRISPR gRNA spacer sequences

    R 0 MIT 0 0 0 Updated Nov 3, 2022
  • crisprViz Public

    Visualization of CRISPR guide RNAs (gRNAs)

    R 1 MIT 0 0 0 Updated Nov 3, 2022
  • crisprDesign Public

    Comprehensive design of CRISPR gRNAs for nucleases and base editors

    R 3 MIT 0 1 0 Updated Nov 3, 2022
  • crisprBase Public

    Base functions and classes for CRISPR gRNA design

    R 0 MIT 0 0 0 Updated Nov 3, 2022

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