rprimer
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see rprimer.
Design Degenerate Oligos from a Multiple DNA Sequence Alignment
Bioconductor version: 3.19
Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.
Author: Sofia Persson [aut, cre] 
Maintainer: Sofia Persson <sofiapersson27 at gmail.com>
citation("rprimer")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rprimer")
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("rprimer")| Instructions for use | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, MultipleSequenceAlignment, SequenceMatching, Software, ddPCR, qPCR |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback |
| System Requirements | |
| URL | https://github.com/sofpn/rprimer |
| Bug Reports | https://github.com/sofpn/rprimer/issues |
See More
| Suggests | BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) |
| 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 | rprimer_1.8.0.tar.gz |
| Windows Binary (x86_64) | rprimer_1.8.0.zip |
| macOS Binary (x86_64) | rprimer_1.8.0.tgz |
| macOS Binary (arm64) | rprimer_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rprimer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rprimer |
| Bioc Package Browser | https://code.bioconductor.org/browse/rprimer/ |
| Package Short Url | https://bioconductor.org/packages/rprimer/ |
| Package Downloads Report | Download Stats |