ddpcr: an R package and web application for analysis of droplet digital PCR data

Dean Attali; Roza Bidshahri; Charles Haynes; Jennifer Bryan

doi:10.12688/f1000research.9022.1

ddpcr: an R package and web application for analysis of droplet digital PCR data

F1000Res. 2016 Jun 17:5:1411. doi: 10.12688/f1000research.9022.1. eCollection 2016.

Authors

Dean Attali¹, Roza Bidshahri², Charles Haynes², Jennifer Bryan³

Affiliations

¹ Bioinformatics Training Program, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
² Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada.
³ Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Statistics, University of British Columbia, Vancouver, Canada.

Abstract

Droplet digital polymerase chain reaction (ddPCR) is a novel platform for exact quantification of DNA which holds great promise in clinical diagnostics. It is increasingly popular due to its digital nature, which provides more accurate quantification and higher sensitivity than traditional real-time PCR. However, clinical adoption has been slowed in part by the lack of software tools available for analyzing ddPCR data. Here, we present ddpcr - a new R package for ddPCR visualization and analysis. In addition, ddpcr includes a web application (powered by the Shiny R package) that allows users to analyze ddPCR data using an interactive graphical interface.

Keywords: Gaussian mixture models; bioinformatics; droplet digital PCR; gating; kernel density estimates; personalized medicine; rpackage; shiny.

Grants and funding

CH receives support as a Canada Research Chair. This work was further supported by the Canadian Institutes of Health Research (CIHR) Bioinformatics Training Program scholarship.