Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.
染色质片段之间的相互作用在功能基因组测定中起重要作用，并且基因组相互作用检测方法的发展已显示基因组内的存在相互作用的拓扑结构域。在这些方法中，Hi-C是起着关键作用的一种重要方法。在这里，我们介绍基因组交互工具和资源平台（GITAR），这是一个执行全面的Hi-C数据分析的软件，软件包括数据预处理，标准化和可视化，以及拓扑相关域（TAD）的分析。 GITAR由两个主要模块组成：（1）HiCtool，一个处理和可视化Hi-C数据的Python库，包括拓扑相关域分析; （2）处理过的Hi-C数据库，使用HiCtool处理的大量人类和小鼠数据集。 HiCtool逐步引导用户完成处理流程，该流程完成从原始Hi-C数据到染色体内接触矩阵和拓扑相关域坐标的计算，可视化，到优化存储整个过程。大量标准化处理数据允许用户以一致的方式比较不同的数据集，同时节省获取可视化或其他分析数据的时间。更重要的是，GITAR可以使没有任何编程或生物信息学专业知识的用户能够使用Hi-C数据。 GITAR在http://genomegitar.org上作为开源软件公开发布。





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