pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research.
pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research.
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DOI：
10.3389/fimmu.2022.954078
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发表时间：
2022
影响因子：
7.3
通讯作者：
Mangul, Serghei
中科院分区：
文献类型：
--
作者：
Peng, Kerui;Moore, Jaden;Vahed, Mohammad;Brito, Jaqueline;Kao, Guoyun;Burkhardt, Amanda M.;Alachkar, Houda;Mangul, Serghei
关键词：
随着T细胞受体库测序（TCR-Seq）技术的进步，T细胞受体（TCR）的研究已经大幅增长。TCR-Seq数据的分析需要计算技能来运行TCR库工具的计算分析。然而，有限的计算背景的生物医学研究人员面临着许多障碍，正确和有效地利用生物信息学工具来分析TCR-Seq数据。在这里，我们报告了pyTCR，一种基于计算笔记本的解决方案，用于全面和可扩展的TCR-Seq数据分析。结合了联合收割机代码、计算和可视化的计算笔记本能够为用户提供高度的灵活性和透明度。此外，计算笔记本电脑被证明是用户友好的，适合于有限的计算技能的研究人员。我们的工具具有丰富的功能，包括各种TCR指标、统计分析和可定制的可视化。pyTCR在大型和多样化的TCR-Seq数据集上的应用将使大规模TCR-Seq数据的有效分析具有灵活性，并最终促进新的发现。
T cell receptor (TCR) studies have grown substantially with the advancement in the sequencing techniques of T cell receptor repertoire sequencing (TCR-Seq). The analysis of the TCR-Seq data requires computational skills to run the computational analysis of TCR repertoire tools. However biomedical researchers with limited computational backgrounds face numerous obstacles to properly and efficiently utilizing bioinformatics tools for analyzing TCR-Seq data. Here we report pyTCR, a computational notebook-based solution for comprehensive and scalable TCR-Seq data analysis. Computational notebooks, which combine code, calculations, and visualization, are able to provide users with a high level of flexibility and transparency for the analysis. Additionally, computational notebooks are demonstrated to be user-friendly and suitable for researchers with limited computational skills. Our tool has a rich set of functionalities including various TCR metrics, statistical analysis, and customizable visualizations. The application of pyTCR on large and diverse TCR-Seq datasets will enable the effective analysis of large-scale TCR-Seq data with flexibility, and eventually facilitate new discoveries.
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作者：
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