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ddPCRclust – An R package and Shiny app for automated analysis of multiplexed ddPCR data

Posted March 15, 2018 | Publications

Brink BG, Meskas J, Brinkman RRBioinformatics. 2018 Mar 9. doi: 10.1093/bioinformatics/bty136. [Epub ahead of print]

Motivation: 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.
Results: 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.
Availability and implementation: R package:; Interface:; Web:
Supplementary information: Supplementary data are available at Bioinformatics online.