PoDCall: positive droplet calling and normalization of droplet digital PCR DNA methylation data

Motivation: Droplet digital PCR (ddPCR) holds great promises for investigating DNA methylation with high sensitivity. Yet, the lack of methods for analyzing ddPCR DNA methylation data has resulted in users processing the data manually at the expense of standardization. Results: PoDCall is an R package performing automated calling of positive droplets, quantification and normalization of methylation levels in ddPCR experiments. A Shiny application provides users with an intuitive and interactive interface to access PoDCall functionalities. Availability and implementation: The PoDCall R package is freely available on Bioconductor at . The Shiny application can be executed from the R console using the wrapper function PoDCall::podcallShiny().

Automated summary

Droplet digital PCR (ddPCR) has the potential for high sensitivity DNA methylation investigation, but the lack of analysis methods has resulted in manual data processing. PoDCall, an R package, automates the calling, quantification, and normalization of methylation levels in ddPCR experiments, providing an intuitive and interactive interface.