CHRONOS

Chronos is a software tool designed to analyze CRISPR loss-of-function screens used in cancer research. These screens involve using CRISPR technology to target specific genes within cells and observe how their removal affects cell growth and proliferation. However, these screens can be affected by various biases and artifacts that can impact the accuracy of the results. To address this issue, Chronos uses computational methods to better model the biological experiment and extract the relevant information from the data. It also incorporates longitudinal CRISPR data and accounts for multiple sources of bias to improve its accuracy. Compared to other methods, Chronos has been shown to perform better across a variety of performance metrics and experimental types.

Topic

Genotype and phenotype;Oncology

Detail

  • Operation: Copy number estimation;Gene expression profiling;RNA-seq read count analysis

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  • Language: Python

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  • Contact: James M. McFarland jmmcfarl@broadinstitute.org

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Publications

  • CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis.
  • Vrahatis AG, et al. CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis. CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis. 2016; 32:884-92. doi: 10.1093/bioinformatics/btv673
  • https://doi.org/10.1093/bioinformatics/btv673
  • PMID: 26568631
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  • Chronos: a CRISPR cell population dynamics model
  • Dempster, J. M.; Boyle, I.; Vazquez, F.; Root, D. E.; Boehm, J. S.; Hahn, W. C.; Tsherniak, A.; McFarland, J. Chronos: a CRISPR cell population dynamics model. bioRxiv 2021. doi: 10.1101/2021.02.25.432728
  • https://doi.org/10.1101/2021.02.25.432728
  • PMID: -
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Download and documentation


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