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openPrimeRui

Shiny Application for Multiplex PCR Primer Design and Analysis


Bioconductor version: Release (3.18)

A Shiny application providing methods for designing, evaluating, and comparing primer sets for multiplex polymerase chain reaction. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected.

Author: Matthias Döring [aut, cre], Nico Pfeifer [aut]

Maintainer: Matthias Döring <matthias-doering at gmx.de>

Citation (from within R, enter citation("openPrimeRui")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("openPrimeRui")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("openPrimeRui")
openPrimeRui HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Software, Technology
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-2
Depends R (>= 4.0.0), openPrimeR(>= 0.99.0)
Imports shiny (>= 1.0.2), shinyjs (>= 0.9), shinyBS (>= 0.61), DT (>= 0.2), rmarkdown (>= 1.0)
System Requirements
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Suggests knitr (>= 1.13)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package openPrimeRui_1.24.0.tar.gz
Windows Binary openPrimeRui_1.24.0.zip (64-bit only)
macOS Binary (x86_64) openPrimeRui_1.24.0.tgz
macOS Binary (arm64) openPrimeRui_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/openPrimeRui
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/openPrimeRui
Bioc Package Browser https://code.bioconductor.org/browse/openPrimeRui/
Package Short Url https://bioconductor.org/packages/openPrimeRui/
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