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Bioconductor - openPrimeR

openPrimeR

This is the released version of openPrimeR; for the devel version, see openPrimeR.

Multiplex PCR Primer Design and Analysis

Bioconductor version: Release (3.21)

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 DÃ¶ring [aut, cre], Nico Pfeifer [aut]

Maintainer: Matthias DÃ¶ring <matthias-doering at gmx.de>

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

To install this package, start R (version "4.5") 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")

Details biocViews Coverage, MultipleComparison, Software, Technology Version 1.29.0 In Bioconductor since BioC 3.6 (R-3.4) (7.5 years) License GPL-2 Depends R (>= 4.0.0) Imports Biostrings(>= 2.38.4), pwalign, 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), 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) System Requirements MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) URL See More Package Archives

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

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