International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Biodata Mining Group, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada.
Bioinformatics. 2018 Aug 1;34(15):2687-2689. doi: 10.1093/bioinformatics/bty136.
Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20 000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high-throughput.
ddPCRclust is an R package for automated analysis of data from Bio-Rad's droplet digital PCR systems (QX100 and QX200). It can automatically analyze and visualize multiplexed ddPCR experiments with up to four targets per reaction. Results are on par with manual analysis, but only take minutes to compute instead of hours. The accompanying Shiny app ddPCRvis provides easy access to the functionalities of ddPCRclust through a web-browser based GUI.
R package: https://github.com/bgbrink/ddPCRclust; Interface: https://github.com/bgbrink/ddPCRvis/; Web: https://bibiserv.cebitec.uni-bielefeld.de/ddPCRvis/.
Supplementary data are available at Bioinformatics online.
液滴数字 PCR（ddPCR）是一种新兴的 DNA 定量技术。通过将目标 DNA 分割成约 20000 个液滴，每个液滴作为其自身的 PCR 反应室，可以实现非常高的 DNA 定量灵敏度。然而，手动分析数据非常耗时，并且没有用于分析非正交、多重 ddPCR 数据的算法，这成为了 ddPCR 从低通量向高通量转变的主要瓶颈。
ddPCRclust 是一个用于分析 Bio-Rad 的液滴数字 PCR 系统（QX100 和 QX200）数据的 R 包。它可以自动分析和可视化每个反应多达四个靶标的多重 ddPCR 实验。结果与手动分析相当，但计算时间只需几分钟，而不是数小时。随附的 Shiny 应用程序 ddPCRvis 通过基于 Web 浏览器的 GUI 提供了对 ddPCRclust 功能的轻松访问。
补充数据可在生物信息学在线获得。
