VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.
VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.
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DOI：
10.3389/fimmu.2018.00976
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发表时间：
2018
影响因子：
7.3
通讯作者：
Cowell LG
中科院分区：
文献类型：
--
作者：
Christley S;Scarborough W;Salinas E;Rounds WH;Toby IT;Fonner JM;Levin MK;Kim M;Mock SA;Jordan C;Ostmeyer J;Buntzman A;Rubelt F;Davila ML;Monson NL;Scheuermann RH;Cowell LG
免疫库测序的最新技术进步为促进我们对各种健康和疾病状态下的适应性免疫反应动力学的理解创造了巨大的潜力。然而，免疫库测序产生大量高度复杂的数据集，这需要专门的方法和软件工具来进行有效的分析和解释。VDJServer是一个基于云的免疫库序列数据分析门户，可访问一套完整分析工作流程的工具，包括序列读数的预处理和质量控制、V（D）J基因片段分配、库表征和库比较等模块。VDJServer还为探索性分析提供了复杂的可视化。它是通过一个标准的网络浏览器，通过一个图形用户界面设计用于免疫学家，临床医生和生物信息学研究人员访问。VDJServer为库测序数据的公共共享以及用户之间数据的私人共享提供了数据共享。我们描述了VDJServer的主要功能和架构，并通过癌症免疫学和自身免疫的用例展示了其功能。VDJServer为人类和小鼠T细胞和B细胞受体库测序数据提供完整的分析套件。其用户友好的界面和高性能计算相结合，无需编程或软件安装即可分析大型免疫组测序项目。VDJServer是一个可通过Web访问的云平台，可通过图形用户界面访问数据管理基础架构、涵盖分析中所有步骤的分析工具集合以及用于共享数据沿着工作流、结果和计算来源的基础架构。VDJServer是一个免费的、公开可用的开源许可资源。
Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.
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影响因子：
8.6
作者：
Johansen, Jorunn N.;Vartdal, Frode;Holmoy, Trygve
通讯作者：
Holmoy, Trygve
影响因子：
--
作者：
Giudicelli, Veronique;Brochet, Xavier;Lefranc, Marie-Paule
通讯作者：
Lefranc, Marie-Paule
影响因子：
7.2
作者：
Cooper ZA;Frederick DT;Juneja VR;Sullivan RJ;Lawrence DP;Piris A;Sharpe AH;Fisher DE;Flaherty KT;Wargo JA
通讯作者：
Wargo JA
影响因子：
7.2
作者：
Jia, Qingzhu;Zhou, Junfeng;Wan, Ying
通讯作者：
Wan, Ying
影响因子：
7
作者：
Freeman, J. Douglas;Warren, Rene L.;Holt, Robert A.
通讯作者：
Holt, Robert A.