Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany.
Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany.
BMC Bioinformatics. 2023 Mar 6;24(1):79. doi: 10.1186/s12859-023-05184-5.
Massive amounts of data are produced by combining next-generation sequencing with complex biochemistry techniques to characterize regulatory genomics profiles, such as protein-DNA interaction and chromatin accessibility. Interpretation of such high-throughput data typically requires different computation methods. However, existing tools are usually developed for a specific task, which makes it challenging to analyze the data in an integrative manner.
We here describe the Regulatory Genomics Toolbox (RGT), a computational library for the integrative analysis of regulatory genomics data. RGT provides different functionalities to handle genomic signals and regions. Based on that, we developed several tools to perform distinct downstream analyses, including the prediction of transcription factor binding sites using ATAC-seq data, identification of differential peaks from ChIP-seq data, and detection of triple helix mediated RNA and DNA interactions, visualization, and finding an association between distinct regulatory factors.
We present here RGT; a framework to facilitate the customization of computational methods to analyze genomic data for specific regulatory genomics problems. RGT is a comprehensive and flexible Python package for analyzing high throughput regulatory genomics data and is available at: https://github.com/CostaLab/reg-gen . The documentation is available at: https://reg-gen.readthedocs.io.
通过将下一代测序与复杂的生物化学技术相结合，可以产生大量数据，以描述调控基因组学特征，如蛋白质-DNA 相互作用和染色质可及性。此类高通量数据的解释通常需要不同的计算方法。然而，现有的工具通常是针对特定任务开发的，这使得以综合的方式分析数据具有挑战性。
我们在这里描述了调控基因组学工具箱（RGT），这是一个用于整合分析调控基因组学数据的计算库。RGT 提供了不同的功能来处理基因组信号和区域。在此基础上，我们开发了几种工具来执行不同的下游分析，包括使用 ATAC-seq 数据预测转录因子结合位点、从 ChIP-seq 数据中识别差异峰、检测三螺旋介导的 RNA 和 DNA 相互作用、可视化以及在不同调控因子之间找到关联。
我们在这里介绍了 RGT；这是一个框架，用于方便定制计算方法，以分析特定调控基因组学问题的基因组数据。RGT 是一个用于分析高通量调控基因组学数据的全面而灵活的 Python 包，可在以下网址获得：https://github.com/CostaLab/reg-gen。文档可在以下网址获得：https://reg-gen.readthedocs.io。
