This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

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

rprimer

This is the development version of rprimer; for the stable release version, see rprimer.

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Bioconductor version: Development (3.18)

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 (from within R, enter citation("rprimer")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Alignment, Coverage, MultipleSequenceAlignment, SequenceMatching, Software, ddPCR, qPCR
Version 1.5.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.1)
Imports Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback
Linking To
Suggests BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/sofpn/rprimer
Bug Reports https://github.com/sofpn/rprimer/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package rprimer_1.5.0.tar.gz
Windows Binary rprimer_1.5.0.zip
macOS Binary (x86_64) rprimer_1.5.0.tgz
macOS Binary (arm64) rprimer_1.5.0.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