# Design Degenerate Oligos from a Multiple DNA Sequence Alignment

## Documentation for package ‘rprimer’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.RprimerAssay | S4 classes for representation of different Rprimer objects
.RprimerMatchAssay | S4 classes for representation of different Rprimer objects
.RprimerMatchOligo | S4 classes for representation of different Rprimer objects
.RprimerOligo | S4 classes for representation of different Rprimer objects
.RprimerProfile | S4 classes for representation of different Rprimer objects
checkMatch | Check how oligos and assays match to their target sequences
checkMatch-method | Check how oligos and assays match to their target sequences
coerce | S4 classes for representation of different Rprimer objects
consensusProfile | Get sequence information from an alignment
designAssays | Design (RT)-PCR assays
designOligos | Design primers and probes
example-datasets | Example datasets
exampleRprimerAlignment | Example datasets
exampleRprimerAssay | Example datasets
exampleRprimerMatchAssay | Example datasets
exampleRprimerMatchOligo | Example datasets
exampleRprimerOligo | Example datasets
exampleRprimerProfile | Example datasets
plotData | Plot an Rprimer object
plotData-method | Plot an Rprimer object
Rprimer-classes | S4 classes for representation of different Rprimer objects
RprimerAssay | S4 classes for representation of different Rprimer objects
RprimerAssay-class | S4 classes for representation of different Rprimer objects
RprimerMatchAssay | S4 classes for representation of different Rprimer objects
RprimerMatchAssay-class | S4 classes for representation of different Rprimer objects
RprimerMatchOligo | S4 classes for representation of different Rprimer objects
RprimerMatchOligo-class | S4 classes for representation of different Rprimer objects
RprimerOligo | S4 classes for representation of different Rprimer objects
RprimerOligo-class | S4 classes for representation of different Rprimer objects
RprimerProfile | S4 classes for representation of different Rprimer objects
RprimerProfile-class | S4 classes for representation of different Rprimer objects
runRprimerApp | rprimer Shiny application