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Keywords {🔍}

genes, pubmed, article, sgrna, crispr, gene, google, scholar, analysis, conditions, mageckvispr, mageckmle, knockout, quality, fig, read, control, screens, central, cas, data, algorithm, screening, distribution, sgrnas, visualization, cell, scores, selected, efficiency, selection, cells, counts, samples, workflow, model, experiments, algorithms, sample, mageck, dataset, essential, vispr, results, design, melanoma, values, day, overrightarrowbetag, sequencing,

Topics {✒️}

}_{jr}{\beta}_{gr}\hfill \end{array} $$ }_{ij}={\beta}_{i0}\hfill \end{array} $$ }_i\left\{\frac{x_{ij}}{{\hat{ }\hbox{'}\overrightarrow{\beta_g^{t-1}}\kern1em \end{array} $$ genome-scale crispr-mediated control data-driven documents crispr-cas9-mediated gene inactivation high-complexity-pooled screen analysis genome-wide crispr screen $$ {\widehat{\sigma}}^2=\widehat{\mu}+ {\beta}_{i0}+{\displaystyle \sum_r}{ ={\beta}_{i0}+{\displaystyle \sum_r}{ {{\widehat{\sigma}}_f}^2 engineered crispr-cas9 complex k-means clustering view =\frac{{\displaystyle {\prod}_j} genome-scale transcriptional activation high-throughput sequencing data employs expectation-maximization }_{jr}{\beta}_{gr} quality control view expectation-maximization gecko hfill \end{array}}} \log dana-farber cancer institute negative binomial model high-throughput sequencing datasets }_i-{\widehat{\mu}}_i article download pdf high-throughput screening gene-level quality control related subjects original author full size image $$ {{\widehat{\sigma}}_i}^2={\left publication-ready svg files genome-wide binding {\overrightarrow{\beta}}_g/se\left myles brown myles brown  myles brown threshold-free enrichment analysis rna-seq read counts crispr-cas9 system = arg\underset{\upbeta_{\mathrm{ expectation-maximization expectation maximization maximum likelihood estimation maximum likelihood approach }_{ij}\sim nb\left {\overrightarrow{\beta^{\ast}}}_g

Schema {🗺️}

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         headline:Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
         description: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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      headline:Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
      description: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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            name:Dana-Farber Cancer Institute
            address:
               name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
               type:PostalAddress
            type:Organization
            name:Tongji University
            address:
               name:School of Life Science and Technology, Tongji University, Shanghai, China
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, USA
      name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
      name:Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, USA
      name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
      name:Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
      name:Broad Institute of MIT and Harvard, Cambridge, USA
      name:Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, USA
      name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
      name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
      name:Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
      name:Department of Statistics, Harvard University, Cambridge, USA
      name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
      name:Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
      name:Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, USA
      name:Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, USA
      name:Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
      name:School of Life Science and Technology, Tongji University, Shanghai, China

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