README.md

In prider: Multiplexed Primer Design by Linear Set Coverage Approximation

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 and Tamminen, 2021.

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)

prider documentation built on March 18, 2022, 8 p.m.