openPrimeR

openPrimeR


openPrimeR is an R package providing methods for designing, evaluating, and comparing primer sets for multiplex polymerase chain reaction (PCR). The package provides a primer design function that generates novel primer sets by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers.

Moreover, existing primer sets can be evaluated according to their coverage and their fulfillment of constraints on the PCR-relevant physicochemical properties. For PCR tasks for which multiple possible primer sets exist, openPrimeR can facilitate the selection of the most suitable set by performing comparative analyses.

The R package includes a Shiny application that provides a comprehensive and intuitive user interface for the core functionalites of the package.




If you have suggestions for improving openPrimeR or if you run into technical problems, please contact mdoering@mpi-inf.mpg.de with a detailed description of your feedback.




News


2017-08-21: openPrimeR version 0.99.0 is publicly available via GitHub.



Installation


To install openPrimeR, please follow the instructions that are provided on our GitHub page. The stand-alone Shiny application is available via Docker.