rprimer
rprimer is a novel R/Bioconductor package to efficiently design degenerate oligos and PCR assays, particularly tailored for sequence-variable viruses. The tool utilizes a multiple DNA sequence alignment as input data and produces comprehensive tables (data frames) and dashboard-like plots as outputs. Users can employ the workflow directly from the R console or through a graphical user interface (Shiny application).
Topic
Probes and primers;PCR experiment;Genotype and phenotype;Sequencing;Workflows
Detail
Operation: PCR primer design;Genotyping;Sequence alignment;Visualisation;Reverse complement
Software interface: Library
Language: R
License: The GNU General Public License v3.0
Cost: Free
Version name: 1.6.0
Credit: Uppsala University, the European Commission, through the European Union reference laboratory for foodborne viruses.
Input: -
Output: -
Contact: Sofia Persson sofiapersson27@gmail.com
Collection: -
Maturity: Stable
Publications
- rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses.
- Persson S, et al. rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. 2022; 23:239. doi: 10.1186/s12859-022-04781-0
- https://doi.org/10.1186/S12859-022-04781-0
- PMID: 35717145
- PMC: PMC9206141
Download and documentation
Source: https://bioconductor.org/packages/release/bioc/src/contrib/rprimer_1.6.0.tar.gz
Documentation: https://bioconductor.org/packages/release/bioc/manuals/rprimer/man/rprimer.pdf
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