PoDCall – Positive Droplet Caller

Digital droplet PCR (ddPCR) is a promising method that can provide a solution for absolute DNA quantification with very high sensitivity, but for DNA methylation data there has been a lack of robust and standardized methods for analyzing such data. We therefore developed PoDCall, an R package that aims to provide a robust calling of positive droplets for DNA methylation ddPCR data performed on the Bio-Rad platform. The package provide functions to read raw two-channel amplitude data exported from either QuantaSoft or QX Manager from a run of ddPCR, set thresholds to call positive droplets and calculate concentrations and normalized concentrations for each well, and write results and optional plots to file. All of the above can be performed either using the functions of PoDCall in a regular R session, or by using the accompanying Shiny app included in the package for a more interactive analysis of the data. The latter allows for visual inspection of the data and results, and also the possibility to manually adjust thresholds if desired. The PoDCall package (Brodal et al, 2023) is available from the Bioconductor repository: https://bioconductor.org/packages/release/bioc/html/PoDCall.html