Prider permits multiplexed oligonucleotide primer and probe design for complex DNA sequence sets by implementing an algorithm for linearly scaling approximation of set coverage. A detailed description available at Smolander et al 2022.
# install.packages("devtools")
devtools::install_github("manutamminen/prider")
test_fasta <- system.file("extdata", "test.fasta", package = "prider")
# Runs Prider with default values
primer_designs <- prider(test_fasta)
# Returns all the primers
primers(primer_designs)
# Returns the primers of a specific primer group
primers(primer_designs)[1]
# Returns all the sequences
sequences(primer_designs)
# Returns the sequence of a specific Id
sequences(primer_designs)[1]
# Plots the primers groups and the target sequences as a heatmap
plot(primer_designs)