openPrimeR

DOI: 10.18129/B9.bioc.openPrimeR    

Multiplex PCR Primer Design and Analysis

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("openPrimeR", version = "3.8")

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 Software, Technology
Version 1.4.1
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), tinytex (>= 0.5)
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_1.4.1.tar.gz
Windows Binary openPrimeR_1.4.1.zip
Mac OS X 10.11 (El Capitan) openPrimeR_1.4.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/openPrimeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/openPrimeR
Package Short Url http://bioconductor.org/packages/openPrimeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: