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@crisprVerse

crisprVerse

Bioconductor ecosystem for CRISPR gRNA design

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, 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

Installation

Requirements

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.

Bioconductor versions

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.

Installing the core crisprVerse 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")

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("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
crisprViz Release OK Devel OK Visualization of CRISPR gRNAs using genomic tracks
crisprShiny Release OK Devel OK Shiny interface for CRISPR gRNAs
screenCounter Release OK Devel OK gRNA barcode sequencing reads alignment tool
Rbwa Release OK Devel OK R wrapper for BWA-backtrack and BWA-MEM aligners

GitHub packages

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

Citation

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}
}

License

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

Pinned Loading

  1. crisprVerse crisprVerse Public

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

    R 12

  2. crisprDesign crisprDesign Public

    Comprehensive design of CRISPR gRNAs for nucleases and base editors

    R 20 6

  3. crisprBase crisprBase Public

    Base functions and classes for CRISPR gRNA design

    R 5

  4. crisprScore crisprScore Public

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

    Python 15 3

  5. crisprDesignData crisprDesignData Public

    Useful human and mouse data for the crisprVerse ecosystem

    R 5

Repositories

Showing 10 of 19 repositories
  • crisprDesignData Public

    Useful human and mouse data for the crisprVerse ecosystem

    crisprVerse/crisprDesignData’s past year of commit activity
    R 5 MIT 0 0 0 Updated Oct 23, 2024
  • crisprDesignAux Public

    Auxiliary functions to the crisprDesign package

    crisprVerse/crisprDesignAux’s past year of commit activity
    R 0 MIT 0 0 0 Updated Oct 23, 2024
  • screenCounter Public

    Get barcode counts from functional genomics screens

    crisprVerse/screenCounter’s past year of commit activity
    C++ 3 MIT 0 1 0 Updated Oct 23, 2024
  • crisprScoreData Public

    Pre-trained models for the crisprScore package

    crisprVerse/crisprScoreData’s past year of commit activity
    R 2 0 0 0 Updated Oct 23, 2024
  • crisprBwa Public

    BWA-based alignment of CRISPR gRNA spacer sequences

    crisprVerse/crisprBwa’s past year of commit activity
    R 1 MIT 0 0 0 Updated Oct 23, 2024
  • crisprBowtie Public

    Bowtie-based alignment of CRISPR gRNA spacer sequences

    crisprVerse/crisprBowtie’s past year of commit activity
    R 3 MIT 0 0 0 Updated Oct 23, 2024
  • crisprScore Public

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

    crisprVerse/crisprScore’s past year of commit activity
    Python 15 MIT 3 6 0 Updated Oct 4, 2024
  • .github Public
    crisprVerse/.github’s past year of commit activity
    0 MIT 0 0 0 Updated Aug 6, 2024
  • Tutorials Public

    Tutorials for the crisprVerse

    crisprVerse/Tutorials’s past year of commit activity
    TeX 10 MIT 0 2 0 Updated Jul 25, 2024
  • crisprBase Public

    Base functions and classes for CRISPR gRNA design

    crisprVerse/crisprBase’s past year of commit activity
    R 5 MIT 0 1 0 Updated Jul 23, 2024