rprimer

DOI: 10.18129/B9.bioc.rprimer  

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Instructions for use
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Coverage, MultipleSequenceAlignment, SequenceMatching, Software, ddPCR, qPCR
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.1)
Imports	Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback
LinkingTo
Suggests	BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/sofpn/rprimer
BugReports	https://github.com/sofpn/rprimer/issues
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_1.2.0.tar.gz
Windows Binary	rprimer_1.2.0.zip
macOS Binary (x86_64)	rprimer_1.2.0.tgz
macOS Binary (arm64)	rprimer_1.2.0.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