Package: rprimer 1.11.0
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:
rprimer_1.11.0.tar.gz
rprimer_1.11.0.zip(r-4.5)rprimer_1.11.0.zip(r-4.4)rprimer_1.11.0.zip(r-4.3)
rprimer_1.11.0.tgz(r-4.4-any)rprimer_1.11.0.tgz(r-4.3-any)
rprimer_1.11.0.tar.gz(r-4.5-noble)rprimer_1.11.0.tar.gz(r-4.4-noble)
rprimer_1.11.0.tgz(r-4.4-emscripten)rprimer_1.11.0.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
- exampleRprimerAlignment - Example datasets
- exampleRprimerAssay - Example datasets
- exampleRprimerMatchAssay - Example datasets
- exampleRprimerMatchOligo - Example datasets
- exampleRprimerOligo - Example datasets
- exampleRprimerProfile - Example datasets
On BioConductor:rprimer-1.11.0(bioc 3.21)rprimer-1.10.0(bioc 3.20)
alignmentddpcrcoveragemultiplesequencealignmentsequencematchingqpcr
Last updated 2 months agofrom:8d5946a5d7. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | NOTE | Dec 18 2024 |
| R-4.3-mac | NOTE | Dec 18 2024 |
Exports:checkMatchconsensusProfiledesignAssaysdesignOligosplotDataRprimerAssayRprimerMatchAssayRprimerMatchOligoRprimerOligoRprimerProfilerunRprimerApp
Dependencies:askpassbase64encBiocGenericsBiostringsbslibcachemclicolorspacecommonmarkcrayoncrosstalkcurldigestDTevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSmathjaxrMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplyrpromisesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4VectorssassscalesshinyshinycssloadersshinyFeedbacksourcetoolsstringistringrsystibbletinytexUCSC.utilsutf8vctrsviridisLitewithrxfunxtableXVectoryamlzlibbioc
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 |
