Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany.
Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany.
Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis.
The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench.
基于 RNA 的调控已成为分子生物学的一个主要研究课题。如果不考虑基于 RNA 的调控，那么对表观遗传和表达数据的分析就是不完整的。因此，将以 RNA 为中心的数据和分析工具与其他类型的实验数据（如 RNA-seq 或 ChIP-seq）相结合变得越来越重要，但尚未成为标准。在这里，我们介绍了 RNA 工作台，这是一套全面的分析工具和整合工作流程，使研究人员能够将这两个世界结合起来。基于 Galaxy 框架，工作台确保了简单的访问、轻松的扩展、灵活适应个人和安全需求，以及独立于命令行知识的复杂分析。目前，它包括 50 多个生物信息学工具，专门用于 RNA 生物学的不同研究领域，包括 RNA 结构分析、RNA 比对、RNA 注释、RNA-蛋白质相互作用、核糖体分析、RNA-seq 分析和 RNA 靶标预测。该工作台由 RNA 生物信息学和 Galaxy 框架方面的专家开发和维护。我们与围绕该工作台不断发展的社区一起，致力于使工作台适应未来的标准和需求，为研究人员提供一个可靠和强大的 RNA 数据分析框架。
RNA 工作台可在 https://github.com/bgruening/galaxy-rna-workbench 上获得。
