The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
Open accessAbstract
High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions. The algorithm uses a generalized linear model to deconvolute different effects, and employs expectation-maximization to iteratively estimate sgRNA knockout efficiency and gene essentiality. MAGeCK-VISPR also includes VISPR, a framework for the interactive visualization and exploration of QC and analysis results. MAGeCK-VISPR is freely available at http://bitbucket.org/liulab/mageck-vispr .
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
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Genome-scale CRISPR-Cas9 knockout screening in human cells
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Streptococcal pyrogenic exotoxin B cleaves GSDMA and triggers pyroptosis
Deng, W., Bai, Y., Deng, F., Pan, Y., Mei, S., Zheng, Z., Min, R., Wu, Z., Li, W., Miao, R., et al. (2022) · Nature · doi:10.1038/s41586-021-04384-4 · Cited by 348
Self-citationCRISPR/Cas9 for cancer research and therapy
Zhan, T., Rindtorff, N., Betge, J., Ebert, M. P., & Boutros, M. (2019) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.04.001 · Cited by 328
Singh, N., Lee, Y. G., Shestova, O., Ravikumar, P., Hayer, K. E., Hong, S. J., Lu, X. M., Pajarillo, R., Agarwal, S., Kuramitsu, S., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0813 · Cited by 295
Metadata
- Authors
- Li, W., Köster, J., Xu, H., Chen, C.-H., Xiao, T., Liu, J. S., Brown, M., & Liu, X. S.
- Venue
- Genome Biology
- Published
- 2015-12
- Volume
- 16
- Issue
- 1
- Pages
- 281-281
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2201689894
- Cited by
- 507
- References
- 38
- FWCI
- 5.27
- Type
- journal article
- Language
- en
- Open access
- gold
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- Li, W., Köster, J., Xu, H., Chen, C.-H., Xiao, T., Liu, J. S., Brown, M., & Liu, X. S. (2015). Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biology. https://doi.org/10.1186/s13059-015-0843-6
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