交互式网络可视化在 Jupyter 笔记本：visJS2jupyter。
Interactive network visualization in Jupyter notebooks: visJS2jupyter.
机构信息
Department of Medicine, Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA.
出版信息
Bioinformatics. 2018 Jan 1;34(1):126-128. doi: 10.1093/bioinformatics/btx581.
MOTIVATION
Network biology is widely used to elucidate mechanisms of disease and biological processes. The ability to interact with biological networks is important for hypothesis generation and to give researchers an intuitive understanding of the data. We present visJS2jupyter, a tool designed to embed interactive networks in Jupyter notebooks to streamline network analysis and to promote reproducible research.
RESULTS
The tool provides functions for performing and visualizing useful network operations in biology, including network overlap, network propagation around a focal set of genes, and co-localization of two sets of seed genes. visJS2jupyter uses the JavaScript library vis.js to create interactive networks displayed within Jupyter notebook cells with features including drag, click, hover, and zoom. We demonstrate the functionality of visJS2jupyter applied to a biological question, by creating a network propagation visualization to prioritize risk-related genes in autism.
AVAILABILITY AND IMPLEMENTATION
The visJS2jupyter package is distributed under the MIT License. The source code, documentation and installation instructions are freely available on GitHub at https://github.com/ucsd-ccbb/visJS2jupyter. The package can be downloaded at https://pypi.python.org/pypi/visJS2jupyter.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
网络生物学被广泛用于阐明疾病和生物过程的机制。与生物网络交互的能力对于假设的产生和帮助研究人员直观地理解数据非常重要。我们提出了 visJS2jupyter，这是一个旨在将交互式网络嵌入 Jupyter 笔记本中的工具，以简化网络分析并促进可重复的研究。
结果
该工具提供了在生物学中执行和可视化有用网络操作的功能，包括网络重叠、围绕一组焦点基因的网络传播以及两个种子基因集的共定位。visJS2jupyter 使用 JavaScript 库 vis.js 创建可在 Jupyter 笔记本单元格中显示的交互式网络，具有拖放、点击、悬停和缩放等功能。我们通过创建网络传播可视化来优先考虑自闭症中的风险相关基因，展示了 visJS2jupyter 在生物学问题中的功能。
可用性和实现
visJS2jupyter 包根据 MIT 许可证分发。源代码、文档和安装说明可在 GitHub 上免费获得，网址为 https://github.com/ucsd-ccbb/visJS2jupyter。该软件包可在 https://pypi.python.org/pypi/visJS2jupyter 下载。
联系方式
补充信息
补充数据可在 Bioinformatics 在线获得。
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