Package: rprimer 1.17.0

Sofia Persson

rprimer: Design Degenerate Oligos from a Multiple DNA Sequence Alignment

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.

Authors:Sofia Persson [aut, cre]

rprimer_1.17.0.tar.gz
rprimer_1.17.0.zip(r-4.7)rprimer_1.17.0.zip(r-4.6)rprimer_1.17.0.zip(r-4.5)
rprimer_1.17.0.tgz(r-4.6-any)rprimer_1.17.0.tgz(r-4.5-any)
rprimer_1.17.0.tar.gz(r-4.7-any)rprimer_1.17.0.tar.gz(r-4.6-any)
rprimer_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rprimer/json (API)

# Install 'rprimer' in R:

install.packages('rprimer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sofpn/rprimer/issues

Datasets:

exampleRprimerAlignment - Example datasets
exampleRprimerAssay - Example datasets
exampleRprimerMatchAssay - Example datasets
exampleRprimerMatchOligo - Example datasets
exampleRprimerOligo - Example datasets
exampleRprimerProfile - Example datasets

On BioConductor:rprimer-1.17.0(bioc 3.24)rprimer-1.16.0(bioc 3.23)

alignment ddpcr coverage multiplesequencealignment sequencematching qpcr

4.81 score 4 stars 16 scripts 347 downloads 11 exports 68 dependencies

Last updated from:beb25279f6. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	198
linux-devel-x86_64	NOTE	287
source / vignettes	OK	258
linux-release-x86_64	NOTE	288
macos-release-arm64	NOTE	144
macos-oldrel-arm64	NOTE	160
windows-devel	NOTE	297
windows-release	NOTE	201
windows-oldrel	NOTE	225
wasm-release	OK	140

Exports:checkMatch consensusProfile designAssays designOligos plotData RprimerAssay RprimerMatchAssay RprimerMatchOligo RprimerOligo RprimerProfile runRprimerApp

Dependencies:base64enc BiocGenerics Biostrings bslib cachem cli commonmark cpp11 crayon crosstalk digest DT evaluate farver fastmap fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httpuv IRanges isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr mathjaxr memoise mime otel patchwork plyr promises R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Vectors S7 sass scales Seqinfo shiny shinycssloaders shinyFeedback sourcetools stringi stringr tinytex vctrs viridisLite withr xfun xtable XVector yaml

Getting started with rprimer

Sofia Persson

Rendered fromgetting-started-with-rprimer.Rmdusingknitr::rmarkdownon May 23 2026.

Last update: 2022-06-21
Started: 2021-10-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check how oligos and assays match to their target sequences	checkMatch checkMatch,RprimerAssay-method checkMatch,RprimerOligo-method
Get sequence information from an alignment	consensusProfile
Design (RT)-PCR assays	designAssays
Design primers and probes	designOligos
Example datasets	example-datasets exampleRprimerAlignment exampleRprimerAssay exampleRprimerMatchAssay exampleRprimerMatchOligo exampleRprimerOligo exampleRprimerProfile
Plot an Rprimer object	plotData plotData,RprimerAssay-method plotData,RprimerMatchAssay-method plotData,RprimerMatchOligo-method plotData,RprimerOligo-method plotData,RprimerProfile-method
S4 classes for representation of different Rprimer objects	.RprimerAssay .RprimerMatchAssay .RprimerMatchOligo .RprimerOligo .RprimerProfile coerce Rprimer-classes RprimerAssay RprimerAssay-class RprimerMatchAssay RprimerMatchAssay-class RprimerMatchOligo RprimerMatchOligo-class RprimerOligo RprimerOligo-class RprimerProfile RprimerProfile-class
rprimer Shiny application	runRprimerApp