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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 (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Instructions for use HTML R Script
Reference Manual PDF


biocViews Alignment, Coverage, MultipleSequenceAlignment, SequenceMatching, Software, ddPCR, qPCR
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.1)
Imports Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback
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Suggests BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package rprimer_1.9.0.tar.gz
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macOS Binary (x86_64) rprimer_1.9.0.tgz
macOS Binary (arm64) rprimer_1.9.0.tgz
Source Repository git clone
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