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Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Bioconductor version: Release (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>

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


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

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


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 1.8.0
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_1.8.0.tar.gz
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macOS Binary (x86_64) rprimer_1.8.0.tgz
macOS Binary (arm64) rprimer_1.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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