openPrimeR

DOI: 10.18129/B9.bioc.openPrimeR    

Multiplex PCR Primer Design and Analysis

Bioconductor version: Release (3.6)

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 <mdoering at mpi-inf.mpg.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("openPrimeR")

Documentation

HTML	R Script	openPrimeR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, Technology
Version	1.0.4
License	GPL-2
Depends	R (>= 3.4.0)
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
Build Report

Package Archives

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

Source Package	openPrimeR_1.0.4.tar.gz
Windows Binary	openPrimeR_1.0.4.zip
Mac OS X 10.11 (El Capitan)	openPrimeR_1.0.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/openPrimeR
Package Short Url	http://bioconductor.org/packages/openPrimeR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive