Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA.
Electrical and Computer Engineering Department, American University of Beirut, Beirut, Lebanon.
Bioinformatics. 2020 Jan 15;36(2):644-646. doi: 10.1093/bioinformatics/btz608.
Visualization of multiple genomic data generally requires the use of public or commercially hosted browsers. Flexible visualization of chromatin interaction data as genomic features and network components offer informative insights to gene expression. An open source application for visualizing HiC and chromatin conformation-based data as 2D-arcs accompanied by interactive network analyses is valuable.
DNA Rchitect is a new tool created to visualize HiC and chromatin conformation-based contacts at high (Kb) and low (Mb) genomic resolutions. The user can upload their pre-filtered HiC experiment in bedpe format to the DNA Rchitect web app that we have hosted or to a version they themselves have deployed. Using DNA Rchitect, the uploaded data allows the user to visualize different interactions of their sample, perform simple network analyses, while also offering visualization of other genomic data types. The user can then download their results for additional network functionality offered in network based programs such as Cytoscape.
DNA Rchitect is freely available both as a web application written primarily in R available at http://shiny.immgen.org/DNARchitect/ and as an open source released under an MIT license at: https://github.com/alosdiallo/DNA_Rchitect.
可视化多个基因组数据通常需要使用公共或商业托管的浏览器。将染色质相互作用数据灵活地可视化作为基因组特征和网络组件，可以为基因表达提供有价值的见解。作为一种用于可视化 HiC 和基于染色质构象数据的开源应用程序，以 2D 弧线形式呈现，并伴随交互式网络分析，是非常有价值的。
DNA Rchitect 是一个新工具，用于可视化高（kb）和低（Mb）基因组分辨率的 HiC 和基于染色质构象的接触。用户可以将其经过预处理的以 bedpe 格式的 HiC 实验上传到我们托管的 DNA Rchitect web 应用程序，或上传到他们自己部署的版本。使用 DNA Rchitect，上传的数据允许用户可视化他们样本的不同相互作用，执行简单的网络分析，同时还提供其他基因组数据类型的可视化。然后，用户可以下载他们的结果，以在 Cytoscape 等基于网络的程序中获得额外的网络功能。
DNA Rchitect 既是一个主要用 R 编写的免费 web 应用程序，可在 http://shiny.immgen.org/DNARchitect/ 访问，也可以作为一个开源项目，根据 MIT 许可证发布：https://github.com/alosdiallo/DNA_Rchitect。
