openPrimeR

DOI: 10.18129/B9.bioc.openPrimeR  

Multiplex PCR Primer Design and Analysis

Bioconductor version: Release (3.16)

An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. 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. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.

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

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

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("openPrimeR")

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("openPrimeR")

 

HTML	R Script	openPrimeR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, MultipleComparison, Software, Technology
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	GPL-2
Depends	R (>= 4.0.0)
Imports	Biostrings(>= 2.38.4), XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges(>= 2.4.8), GenomicRanges(>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER(>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics(>= 0.16.1), S4Vectors(>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), distr (>= 2.6), distrEx (>= 2.6), fitdistrplus (>= 1.0-7), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0)
LinkingTo
Suggests	testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9)
SystemRequirements	MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3)
Enhances
URL
Depends On Me	openPrimeRui
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	openPrimeR_1.20.0.tar.gz
Windows Binary	openPrimeR_1.20.0.zip (64-bit only)
macOS Binary (x86_64)	openPrimeR_1.20.0.tgz
macOS Binary (arm64)	openPrimeR_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/openPrimeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/openPrimeR
Bioc Package Browser	https://code.bioconductor.org/browse/openPrimeR/
Package Short Url	https://bioconductor.org/packages/openPrimeR/
Package Downloads Report	Download Stats