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PoDCall: positive droplet calling and normalization of droplet digital PCR DNA methylation data
Marine Jeanmougin1, Hans Petter Brodal1, Heidi Dietrichson Pharo1,2
1Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo 0379, Norway.
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 https://bioconductor.org/packages/PoDCall/. The Shiny application can be executed from the R console using the wrapper function PoDCall::podcallShiny().
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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