Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine.
Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine.
复制标题
诊所中的棒棒糖：精密医学的信息致密突变图。
DOI：
10.1371/journal.pone.0160519
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Brouwer C
中科院分区：
文献类型：
--
作者：
Jay JJ;Brouwer C
简洁的可视化对于在最小的空间内呈现大量可以快速解释的信息至关重要。尽管可视化在整个生命科学中越来越必要，但由于解释的时间依赖性，精准医学的临床应用呈现出重要的用例。在本文中，我们描述了用于呈现面板或外显子组测序结果的 Lollipop 软件。源代码和二进制文件可在 https://github.com/pbnjay/lollipops 上免费获取。尽管存在其他软件和网络资源来生成棒棒糖图，但这些软件包不太适合临床应用。精准医疗的需求需要能够轻松融入工作流程并整合外部信息，而无需人工干预。 Lollipops 软件提供了一个简单的命令行界面，只需要官方的基因符号和突变列表，使其易于编写脚本。使用公开的 Uniprot 和 Pfam 资源集成外部信息。启发式方法用于选择信息最丰富的组件并将它们浓缩成简洁的图。输出是灵活的可缩放矢量图形 (SVG)，可以在网页或图形插图工具中显示。 Lollipops 软件为精准医学的自动化流程和高通量工作流程创建信息密集、出版质量的突变图。自动数据集成可确保临床数据安全，可视化启发法以最少的用户配置简洁地呈现知识。
Concise visualization is critical to present large amounts of information in a minimal space that can be interpreted quickly. Clinical applications in precision medicine present an important use case due to the time dependent nature of the interpretations, although visualization is increasingly necessary across the life sciences. In this paper we describe the Lollipops software for the presentation of panel or exome sequencing results. Source code and binaries are freely available at https://github.com/pbnjay/lollipops. Although other software and web resources exist to produce lollipop diagrams, these packages are less suited to clinical applications. The demands of precision medicine require the ability to easily fit into a workflow and incorporate external information without manual intervention. The Lollipops software provides a simple command line interface that only requires an official gene symbol and mutation list making it easily scriptable. External information is integrated using the publicly available Uniprot and Pfam resources. Heuristics are used to select the most informative components and condense them for a concise plot. The output is a flexible Scalable Vector Graphic (SVG) diagram that can be displayed in a web page or graphic illustration tool. The Lollipops software creates information-dense, publication-quality mutation plots for automated pipelines and high-throughput workflows in precision medicine. The automatic data integration enables clinical data security, and visualization heuristics concisely present knowledge with minimal user configuration.