openPrimeR
Multiplex PCR Primer Design and Analysis
Bioconductor version: Release (3.20)
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>
citation("openPrimeR")):
Installation
To install this package, start R (version "4.4") 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")| openPrimeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, MultipleComparison, Software, Technology |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | openPrimeR_1.28.0.tar.gz |
| Windows Binary (x86_64) | openPrimeR_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | openPrimeR_1.28.0.tgz |
| macOS Binary (arm64) | openPrimeR_1.27.0.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 |