Introduction | Installation | Overview | Shiny application | Workflow | Collection of target sequences and multiple alignment | Data import | Design procedure | Step 1: consensusProfile | Step 2: designOligos | Design with default settings | Design with modified settings, and mixed primers | Scoring system | Visualize oligo binding regions | Step 3: designAssays | Further handling of the data | Oligo and assay binding regions | Check match | Export to file | Result tables | Fasta-format | Summary | Classes and example data | Table values | Source code | Citation | Session info | References
Package: rprimer 1.17.3
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_1.17.3.tar.gz
rprimer_1.17.3.zip(r-4.7-any)rprimer_1.17.3.zip(r-4.6-any)rprimer_1.17.3.zip(r-4.5-any)
rprimer_1.17.3.tgz(r-4.6-any)rprimer_1.17.3.tgz(r-4.5-any)
rprimer_1.17.3.tar.gz(r-4.7-any)rprimer_1.17.3.tar.gz(r-4.6-any)
rprimer_1.17.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
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-1.17.3(bioc 3.24)rprimer-1.16.0(bioc 3.23)
alignmentddpcrcoveragemultiplesequencealignmentsequencematchingqpcr
Last updated from:f1615e1f6f. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 182 | ||
| linux-devel | NOTE | 333 | ||
| source / vignettes | OK | 257 | ||
| linux-release | NOTE | 362 | ||
| macos-release | NOTE | 206 | ||
| macos-oldrel | NOTE | 187 | ||
| windows-devel | NOTE | 218 | ||
| windows-release | NOTE | 207 | ||
| windows-oldrel | NOTE | 202 | ||
| wasm-release | OK | 143 |
Exports:checkMatchconsensusProfiledesignAssaysdesignOligosplotDataRprimerAssayRprimerMatchAssayRprimerMatchOligoRprimerOligoRprimerProfilerunRprimerApp
Dependencies:base64encBiocGenericsBiostringsbslibcachemclicommonmarkcpp11crayoncrosstalkdigestDTevaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvIRangesisobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagrittrmathjaxrmemoisemimeMultipleAlignmentotelpatchworkplyrpromisesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4VectorsS7sassscalesSeqinfoshinyshinycssloadersshinyFeedbacksourcetoolsstringistringrtinytexvctrsviridisLitewithrxfunxtableXVectoryaml
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 |
