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rprimer

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Bioconductor version: Release (3.17)

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")

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 1.4.0
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_1.4.0.tar.gz
Windows Binary rprimer_1.4.0.zip
macOS Binary (x86_64) rprimer_1.4.0.tgz
macOS Binary (arm64) rprimer_1.4.0.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