API for sofpn/rprimer
Design Degenerate Oligos from a Multiple DNA Sequence Alignment
| Global functions | |
|---|---|
| .RprimerAssay | Man page |
| .RprimerMatchAssay | Man page |
| .RprimerMatchOligo | Man page |
| .RprimerOligo | Man page |
| .RprimerProfile | Man page |
| .addEmptyRow | Source code |
| .addNames | Source code |
| .addProbes | Source code |
| .allVariants | Source code |
| .asIUPAC | Source code |
| .assayFeaturePlot | Source code |
| .assayPlot | Source code |
| .barPlot | Source code |
| .beautifyOligos | Source code |
| .beautifyPrimers | Source code |
| .beautifyProbes | Source code |
| .boxPlot | Source code |
| .checkMatchAssay | Source code |
| .checkMatchOligo | Source code |
| .checkPrimers | Source code |
| .checkProbes | Source code |
| .combinePrimers | Source code |
| .consensusMatrix | Source code |
| .convertAssay | Source code |
| .convertToMatrices | Source code |
| .countDegeneracy | Source code |
| .coverage | Source code |
| .deltaG | Source code |
| .designAmbiguousOligos | Source code |
| .designMixedPrimers | Source code |
| .dnaBasesOnly | Source code |
| .dotPlot | Source code |
| .endRuns | Source code |
| .expandDegenerates | Source code |
| .extractProbes | Source code |
| .filterOligos | Source code |
| .filterPrimers | Source code |
| .filterProbes | Source code |
| .findMostCommonBase | Source code |
| .gapPlot | Source code |
| .gcClamp | Source code |
| .gcPlot | Source code |
| .gcTmCoveragePlot | Source code |
| .generateAmbiguousOligos | Source code |
| .generateMixedOligos | Source code |
| .getMatchIndex | Source code |
| .getMatchProportion | Source code |
| .getSequenceNames | Source code |
| .hideXYAxes | Source code |
| .highlightRegion | Source code |
| .identifyMask | Source code |
| .identifyProbes | Source code |
| .identityPlot | Source code |
| .initiate | Source code |
| .isValid | Source code |
| .isWithinRange | Source code |
| .iupacConsensus | Source code |
| .majorityConsensus | Source code |
| .makeOligoDf | Source code |
| .maskRange | Source code |
| .maskRegion | Source code |
| .meanRange | Source code |
| .mergeLists | Source code |
| .mixFwd | Source code |
| .mixRev | Source code |
| .nmers | Source code |
| .nn | Source code |
| .nucleotideIdentity | Source code |
| .oligoFeaturePlot | Source code |
| .oligoMatrix | Source code |
| .oligoPlot | Source code |
| .pairPrimers | Source code |
| .plotMatch | Source code |
| .plotMatchAssay | Source code |
| .plotNucleotides | Source code |
| .plotOverview | Source code |
| .primerPlot | Source code |
| .primerProbePlot | Source code |
| .probePlot | Source code |
| .repeats | Source code |
| .reverseComplement | Source code |
| .runningAverage | Source code |
| .scoreGcContent | Source code |
| .scoreIdentityCoverage | Source code |
| .scoreOligos | Source code |
| .showXAxisHideYAxis | Source code |
| .showXYAxes | Source code |
| .showYAxisHideXAxis | Source code |
| .splitAndPaste | Source code |
| .splitOligoDf | Source code |
| .stack | Source code |
| .themeRprimer | Source code |
| .tm | Source code |
| .tmParameters | Source code |
| .toDNAStringSetAssay | Source code |
| .toDNAStringSetOligo | Source code |
| .uniqueSequences | Source code |
| .violinPlot | Source code |
| Rprimer-classes | Man page |
| RprimerAssay | Man page Source code |
| RprimerAssay-class | Man page |
| RprimerMatchAssay | Man page Source code |
| RprimerMatchAssay-class | Man page |
| RprimerMatchOligo | Man page Source code |
| RprimerMatchOligo-class | Man page |
| RprimerOligo | Man page Source code |
| RprimerOligo-class | Man page |
| RprimerProfile | Man page Source code |
| RprimerProfile-class | Man page |
| arrangeMask | Source code |
| assayFilterServer | Source code |
| assayFilterUI | Source code |
| assayServer | Source code |
| assayUI | Source code |
| checkMatch | Man page |
| checkMatch,RprimerAssay-method | Man page |
| checkMatch,RprimerOligo-method | Man page |
| coerce | Man page |
| consensusProfile | Man page Source code |
| consensusServer | Source code |
| consensusUI | Source code |
| conservationInput | Source code |
| convertToOligo | Source code |
| dataServer | Source code |
| dataUI | Source code |
| designAssays | Man page Source code |
| designOligos | Man page Source code |
| example-datasets | Man page |
| exampleRprimerAlignment | Man page |
| exampleRprimerAssay | Man page |
| exampleRprimerMatchAssay | Man page |
| exampleRprimerMatchOligo | Man page |
| exampleRprimerOligo | Man page |
| exampleRprimerProfile | Man page |
| filterOligos | Source code |
| makeEmptyRow | Source code |
| makeListTable | Source code |
| makeRc | Source code |
| makeRcList | Source code |
| nextButton | Source code |
| numericInputFrom | Source code |
| numericInputTo | Source code |
| oligoFilterServer | Source code |
| oligoFilterUI | Source code |
| oligoServer | Source code |
| oligoUI | Source code |
| plotData | Man page |
| plotData,RprimerAssay-method | Man page |
| plotData,RprimerMatchAssay-method | Man page |
| plotData,RprimerMatchOligo-method | Man page |
| plotData,RprimerOligo-method | Man page |
| plotData,RprimerProfile-method | Man page |
| previousButton | Source code |
| removeListColumns | Source code |
| roundDbls | Source code |
| rprimer | Man page |
| rprimer-package | Man page |
| rprimerApp | Source code |
| runRprimerApp | Man page Source code |
| spinnerPlot | Source code |
| splitAssayToList | Source code |
| switchPage | Source code |
| welcomeUI | Source code |
