Li Yan, Andrade Jorge
Center for Research Informatics, University of Chicago, Knapp Center for Biomedical Discovery, 900 East 57th St., Chicago, 60637 USA.
Source Code Biol Med. 2017 Feb 3;12:2. doi: 10.1186/s13029-017-0063-4. eCollection 2017.
A 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.
We 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.
DEApp 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/DEAppand https://gallery.shinyapps.io/DEApp.
生物医学领域的一个发展趋势是在基因组学研究中使用下一代测序（NGS）技术。然而，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编程和命令行知识。此外，研究人员通常需要交互式地评估和可视化使用不同统计和误差模型的效果，评估选择不同参数和截止值的影响，最后探索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，减缓或阻碍了许多实验室采用NGS技术。
我们开发了DEApp，这是一个用于基于计数的NGS数据差异表达分析的交互式动态网络应用程序。该应用程序在用户友好的界面中实现了模型选择、参数调整、交叉验证和结果可视化。
DEApp使没有全职生物信息学家的实验室能够在生物医学研究中利用NGS应用的优势。该应用程序可在https://yanli.shinyapps.io/DEApp和https://gallery.shinyapps.io/DEApp免费获取。
