README.md

CRAN status

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)



Try the prider package in your browser

Any scripts or data that you put into this service are public.

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