BioConductor
openPrimeR 1.2.0
Multiplex PCR Primer Design and Analysis
Released May 1, 2018 by Matthias Döring
Dependencies
distrEx 2.7.0 distr 2.7.0 dplyr 0.7.6 seqinr 3.4-5 foreach 1.4.4 uniqtag 1.0 S4Vectors 0.18.3 Biostrings 2.48.0 ape 5.1 magrittr 1.5 IRanges 2.14.10 stringdist 0.9.5.1 XML 3.98-1.16 RColorBrewer 1.1-2 stringr 1.3.1 Hmisc 4.1-1 openxlsx 4.1.0 DECIPHER 2.8.1 plyr 1.8.4 reshape2 1.4.3 ggplot2 3.0.0 scales 1.0.0 GenomicRanges 1.32.6 BiocGenerics 0.26.0 digest 0.6.16 fitdistrplus 1.0-9 lpSolveAPI 5.5.2.0-17
An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.