Multiplexed Primer Design by Linear Set Coverage Approximation

Implementation of an oligonucleotide primer and probe design algorithm using a linearly scaling approximation of set coverage. A detailed description available at Smolander and Tamminen, 2021; .

Prider

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.

Installation

# install.packages("devtools")
devtools::install_github("manutamminen/prider")

Examples

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)