ArticleBioinformatics (Oxford, England)2024
Guide assignment in single-cell CRISPR screens using crispat.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Article
- Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells.Nature biotechnology · 2026Article
- ScalablebioRxiv : the preprint server for biology · 2026Article
- Article
- Targeted single-cell RNA and perturbation sequencing with TAP-seq.Nature protocols · 2026Review
- A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines.Cell genomics · 2026Article
- Pertpy: an end-to-end framework for perturbation analysis.Nature methods · 2026Article
- Dissecting cellular ecosystem with single-cell CRISPR screens.Blood science (Baltimore, Md.) · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
motivationPooled single-cell CRISPR screens have emerged as a powerful tool in functional genomics to probe the effect of genetic interventions at scale. A crucial step in the analysis of the resulting data is the assignment of cells to gRNAs corresponding to a specific genetic intervention. However, this step is challenging due to a lack of systematic benchmarks and accessible software to apply and compare different guide assignment strategies. To address this, we here propose crispat (CRISPR guide assignment tool), a Python package to facilitate the choice of a suitable guide assignment strategy for single-cell CRISPR screens.
resultsWe demonstrate the package on four single-cell CRISPR interference screens at low multiplicity of infection from two studies, where crispat identifies strong differences in the number of assigned cells, downregulation of the target genes and number of discoveries across different guide assignment strategies, highlighting the need for a suitable guide assignment strategy to obtain optimal power in single-cell CRISPR screens. AVAILABILITY AND IMPLEMENTATION: crispat is implemented in python, the source code, installation instructions and tutorials can be found at https://github.com/velten-group/crispat and it can be installed from PyPI (https://pypi.org/project/crispat/). Code to reproduce all findings in this paper is available at https://github.com/velten-group/crispat_analysis, as well as at https://zenodo.org/records/13373265.
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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.