rprimer
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 (3.24)
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 gmail.com>
citation("rprimer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Instructions for use | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, MultipleSequenceAlignment, SequenceMatching, Software, ddPCR, qPCR |
| Version | 1.17.3 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.6.0), Biostrings, MultipleAlignment |
| Imports | 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
| Suggests | BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rprimer_1.17.3.tar.gz |
| Windows Binary (x86_64) | rprimer_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | rprimer_1.17.3.tgz |
| macOS Binary (sonoma-arm64) | rprimer_1.17.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rprimer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rprimer |
| Bioc Package Browser | https://code.bioconductor.org/browse/rprimer/ |
| Package Short Url | https://bioconductor.org/packages/rprimer/ |
| Package Downloads Report | Download Stats |