# sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

## Documentation for package ‘sangeranalyseR’ version 1.23.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

ChromatogramParam-class | ChromatogramParam
chromatogram_overwrite | Static base-R chromatogram renderer with a corrected color palette.
chromatogram_plotly | Render a Sanger chromatogram as an interactive Plotly widget
generateReport | Method generateReport
generateReportSA | Method generateReportSA
generateReportSA-method | generateReportSA
generateReportSC | Method generateReportSC
generateReportSC-method | generateReportSC
generateReportSR | Method generateReportSR
generateReportSR-method | generateReportSR
globalTrimApp | Launch a global trimming controls dashboard
launchApp | Method launchApp
launchAppSA | Method launchAppSA
launchAppSA-method | launchAppSA
launchAppSC | Method launchAppSC
launchAppSC-method | launchAppSC
MakeBaseCalls | Method MakeBaseCalls
MakeBaseCalls-method | MakeBaseCalls
ObjectResults-class | ObjectResults
primaryAASeqS1 | Method primaryAASeqS1
primaryAASeqS1-method | Method primaryAASeqS1
primaryAASeqS2 | Method primaryAASeqS2
primaryAASeqS2-method | Method primaryAASeqS2
primaryAASeqS3 | Method primaryAASeqS3
primaryAASeqS3-method | Method primaryAASeqS3
qualityBasePlot | Method qualityBasePlot
qualityBasePlot-method | qualityBasePlot
qualityBasePlot-method | qualityBasePlot
QualityReport-class | QualityReport
QualityReport-class-qualityBasePlot | qualityBasePlot
QualityReport-class-updateQualityParam | updateQualityParam
qualityReportData | QualityReport instance
readTable | Method readTable
readTable-method | readTable
readTable-method | readTable
SangerAlignment | SangerAlignment
SangerAlignment-class | SangerAlignment
SangerAlignment-class-generateReportSA | generateReportSA
SangerAlignment-class-launchAppSA | launchAppSA
SangerAlignment-class-updateQualityParam | updateQualityParam
SangerAlignment-class-writeFastaSA | writeFastaSA
sangerAlignmentData | SangerAlignment instance
sangeranalyseR | sangeranalyseR-package
SangerContig | SangerContig
SangerContig-class | SangerContig
SangerContig-class-generateReportSC | generateReportSC
SangerContig-class-launchAppSC | launchAppSC
SangerContig-class-readTable | readTable
SangerContig-class-updateQualityParam | updateQualityParam
SangerContig-class-writeFastaSC | writeFastaSC
sangerContigData | SangerContig instance
SangerRead | SangerRead
SangerRead-class | SangerRead
SangerRead-class-generateReportSR | generateReportSR
SangerRead-class-MakeBaseCalls | MakeBaseCalls
SangerRead-class-qualityBasePlot | qualityBasePlot
SangerRead-class-readTable | readTable
SangerRead-class-updateQualityParam | updateQualityParam
SangerRead-class-writeFastaSR | writeFastaSR
sangerReadFData | SangerRead instance
updateQualityParam | Method updateQualityParam
updateQualityParam-method | updateQualityParam
updateQualityParam-method | updateQualityParam
updateQualityParam-method | updateQualityParam
updateQualityParam-method | updateQualityParam
writeFasta | Method writeFasta
writeFastaSA | Method writeFastaSA
writeFastaSA-method | writeFastaSA
writeFastaSC | Method writeFastaSC
writeFastaSC-method | writeFastaSC
writeFastaSR | Method writeFastaSR
writeFastaSR-method | writeFastaSR