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Bioconductor - rprimer

rprimer

This is the released version of rprimer; for the devel version, see rprimer.

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Bioconductor version: Release (3.21)

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] ORCID: 0000-0003-2611-3030

Maintainer: Sofia Persson <sofiapersson27 at gmail.com>

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

To install this package, start R (version "4.5") 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")
Details biocViews Alignment, Coverage, MultipleSequenceAlignment, SequenceMatching, Software, ddPCR, qPCR Version 1.12.0 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License GPL-3 Depends R (>= 4.1) Imports Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback System Requirements URL https://github.com/sofpn/rprimer Bug Reports https://github.com/sofpn/rprimer/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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