openPrimeR
Multiplex PCR Primer Design and Analysis
Bioconductor version: 3.23 · Package version: 1.34.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("openPrimeR")Details
| Maintainer | Matthias Döring <matthias-doering@gmx.de> |
| Author | Matthias Döring [aut, cre], Nico Pfeifer [aut] |
| License | GPL-2 |
| System Requirements | MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) |
| Downloads rank | 578 |
| Source branch | RELEASE_3_23 |
| biocViews | Coverage, MultipleComparison, Software, Technology |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | openPrimeR_1.34.0.tar.gz |
| Windows binary (x86_64) | openPrimeR_1.34.0.zip |
| macOS binary (arm64) | openPrimeR_1.34.0.tgz |
| macOS binary (x86_64) | openPrimeR_1.34.0.tgz |
Dependencies
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)
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)