ArticleNature communications2022
A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Genomic repeats for single-cell molecular recording.bioRxiv : the preprint server for biology · 2026Article
- Upper bound on the mutational burden imposed by a CRISPR-Cas9 gene-drive element.G3 (Bethesda, Md.) · 2026Article
- Adenine base editor for knockout of proteins: A practical guide from design to analysis with updated MultiEditRbatch.Molecular therapy. Nucleic acids · 2026Article
- A tunable Cas12a platform for single-cell perturbation screening and CRISPRi.Nature communications · 2026Article
- Template-driven scaffolding of SCFNature · 2026Article
- PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design.bioRxiv : the preprint server for biology · 2026Article
- JMJD2 regulates enhancer-promoter interactions via biomolecular condensate formation.Nature genetics · 2026Article
- Optimization of functional genetics tools for a model tetraploid Capsella bursa-pastoris, with focus on homoeolog-aware gene editing.Transgenic research · 2026Article
- Comprehensive web-based platform for advanced PCR design, genotyping, synthetic biology, molecular diagnostics, and sequence analysis.Molecular therapy. Nucleic acids · 2025Article
- Single-molecule live-cell RNA imaging with CRISPR-Csm.Nature biotechnology · 2025Article
- Pseudokinase STK40 limits T cell exhaustion through COP1-dependent degradation of AP1-family transcription factors.Nature immunology · 2025Article
- CRISPR-based Transcriptional Regulation: Technologies, Applications, and Future Directions.DNA · 2025Article
- Transcription factor Zfx regulates tumor's evasion to T cell killing in immunotherapy.iScience · 2025Article
- A compendium of synthetic lethal gene pairs defined by extensive combinatorial pan-cancer CRISPR screening.Genome biology · 2025Article
- Anti-RNA virus crRNA targets efficient screening platform based on bioinformatics and CRISPR detection.Molecular therapy. Nucleic acids · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- CRISPR-BEasy: a free web-based service for designing sgRNA tiling libraries for CRISPR-dependent base editing screens.Nucleic acids research · 2025Article
- Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.Nature biotechnology · 2025Article
- CRISPRware: a software package for contextual gRNA library design.BMC genomics · 2025Article
- A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular anti-sense oligonucleotide activity.Nature communications · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crisprVerse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe) and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a user-friendly and unified interface to add off-target annotations, rich gene and SNP annotations, and on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. The crisprVerse ecosystem is open-source and deployed through the Bioconductor project ( https://github.com/crisprVerse ).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.