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DEApp: an interactive web interface for differential expression analysis of next generation sequence data

机译：DEApp：交互式Web界面，用于下一代序列数据的差异表达分析

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BackgroundA growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is however still challenging, as it requires sufficient computer programing and command-line knowledge. Furthermore, researchers often need to evaluate and visualize interactively the effect of using differential statistical and error models, assess the impact of selecting different parameters and cutoffs, and finally explore the overlapping consensus of cross-validated results obtained with different methods. This represents a bottleneck that slows down or impedes the adoption of NGS technologies in many labs. ResultsWe developed DEApp, an interactive and dynamic web application for differential expression analysis of count based NGS data. This application enables models selection, parameter tuning, cross validation and visualization of results in a user-friendly interface. ConclusionsDEApp enables labs with no access to full time bioinformaticians to exploit the advantages of NGS applications in biomedical research. This application is freely available at https://yanli.shinyapps.io/DEApp and https://gallery.shinyapps.io/DEApp .
机译：背景技术生物医学界的一个增长趋势是在基因组学研究中使用下一代测序（NGS）技术。但是，下游差异表达（DE）分析的复杂性仍然具有挑战性，因为它需要足够的计算机程序设计和命令行知识。此外，研究人员经常需要评估和可视化使用差分统计和误差模型的效果，评估选择不同参数和临界值的影响，最后探索使用不同方法获得的交叉验证结果的重叠共识。这是一个瓶颈，它会减慢或阻碍许多实验室采用NGS技术。结果我们开发了DEApp，这是一个交互式的动态Web应用程序，用于基于计数的NGS数据的差异表达分析。该应用程序可在用户友好的界面中进行模型选择，参数调整，交叉验证和结果可视化。结论DEApp使无法接触专职生物信息学家的实验室能够利用NGS应用在生物医学研究中的优势。该应用程序可从https://yanli.shinyapps.io/DEApp和https://gallery.shinyapps.io/DEApp免费获得。

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