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# 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](https://link.springer.com/article/10.1186/s12859-022-04710-1).

## Installation

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

```

## Examples

```R
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)

```
