Package: rprimer 1.9.0

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_1.9.0.tar.gz
rprimer_1.9.0.zip(r-4.5)rprimer_1.9.0.zip(r-4.4)rprimer_1.9.0.zip(r-4.3)
rprimer_1.9.0.tgz(r-4.4-any)rprimer_1.9.0.tgz(r-4.3-any)
rprimer_1.9.0.tar.gz(r-4.5-noble)rprimer_1.9.0.tar.gz(r-4.4-noble)
rprimer_1.9.0.tgz(r-4.4-emscripten)rprimer_1.9.0.tgz(r-4.3-emscripten)
rprimer.pdf |rprimer.html✨
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-1.9.0(bioc 3.20)rprimer-1.8.0(bioc 3.19)

bioconductor-package

11 exports 0.61 score 84 dependencies

Last updated 2 months agofrom:dd88cec5fd

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

Dependencies:askpass base64enc BiocGenerics Biostrings bslib cachem cli colorspace commonmark crayon crosstalk curl digest DT evaluate fansi farver fastmap fontawesome fs GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS mathjaxr Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plyr promises R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Vectors sass scales shiny shinycssloaders shinyFeedback sourcetools stringi stringr sys tibble tinytex UCSC.utils utf8 vctrs viridisLite withr xfun xtable XVector yaml zlibbioc

Getting started with rprimer

Sofia Persson

Rendered fromgetting-started-with-rprimer.Rmdusingknitr::rmarkdownon Jun 30 2024.

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