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

Package index
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Vignettes
Functions
153
Source code
45
Man pages
44
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sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
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API

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

Global functions
.onAttach Source code
ChromatogramParam-class Man page
M1inside_calculate_trimming Source code
M2inside_calculate_trimming Source code
MakeBaseCalls Man page
MakeBaseCalls,SangerRead-method Man page
MakeBaseCallsInside Source code
PrimAASeqS1Display Source code
PrimAASeqS2Display Source code
PrimAASeqS3Display Source code
QualityBasePlotly Source code
QualityReport-class Man page
QualityReport-class-qualityBasePlot Man page
QualityReport-class-updateQualityParam Man page
SangerAlignment Man page Source code
SangerAlignment-class Man page
SangerAlignment-class-generateReportSA Man page
SangerAlignment-class-launchAppSA Man page
SangerAlignment-class-updateQualityParam Man page
SangerAlignment-class-writeFastaSA Man page
SangerAlignmentServer Source code
SangerContig Man page Source code
SangerContig-class Man page
SangerContig-class-generateReportSC Man page
SangerContig-class-launchAppSC Man page
SangerContig-class-updateQualityParam Man page
SangerContig-class-writeFastaSC Man page
SangerContigServer Source code
SangerRead Man page Source code
SangerRead-class Man page
SangerRead-class-MakeBaseCalls Man page
SangerRead-class-generateReportSR Man page
SangerRead-class-qualityBasePlot Man page
SangerRead-class-readTable Man page
SangerRead-class-updateQualityParam Man page
SangerRead-class-writeFastaSR Man page
SangerReadInnerTrimming Source code
SetAllStyleList Source code
SetCharStyleList Source code
alignContigs Source code
calculateAASeq Source code
calculateContigSeq Source code
checkAb1FastaCsv Source code
checkAcceptStopCodons Source code
checkBaseNumPerRow Source code
checkFastaFileName Source code
checkGeneticCode Source code
checkHeightPerRow Source code
checkInputSource Source code
checkMaxFractionLost Source code
checkMinFractionCall Source code
checkMinReadLength Source code
checkMinReadsNum Source code
checkParentDirectory Source code
checkProcessorsNum Source code
checkQualityPhredScores Source code
checkReadFeature Source code
checkReadFileName Source code
checkReadingFrame Source code
checkShowTrimmed Source code
checkSignalRatioCutoff Source code
checkTrimParam Source code
chromatogramRowNum Source code
chromatogram_overwrite Source code
countCoincidentSp Source code
countStopSodons Source code
dynamicMenuSideBarSA Source code
dynamicMenuSideBarSC Source code
generateReport Man page Source code
generateReportSA Man page
generateReportSA,SangerAlignment-method Man page
generateReportSC Man page
generateReportSC,SangerContig-method Man page
generateReportSR Man page
generateReportSR,SangerRead-method Man page
getIndelDf Source code
getProcessors Source code
getpeaks Source code
indelRow Source code
launchApp Man page Source code
launchAppSA Man page
launchAppSA,SangerAlignment-method Man page
launchAppSC Man page
launchAppSC,SangerContig-method Man page
nPairwiseDiffs Source code
observeEventDynamicHeaderSC Source code
oneAmbiguousColumn Source code
peakvalues Source code
preQualityBasePlot Source code
primarySeqDisplay Source code
primarySeqTrimmedDisplay Source code
qualityBasePlot Man page
qualityBasePlot,QualityReport-method Man page
qualityBasePlot,SangerRead-method Man page
qualityQualityBasePlotDisplay Source code
qualityReportData Man page
qualityScoreDisplay Source code
readTable Man page
readTable,SangerRead-method Man page
sangerAlignmentData Man page
sangerContigData Man page
sangerReadFData Man page
sangeranalyseR Man page
secondSeqTrimmedDisplay Source code
secondarySeqDisplay Source code
suppressPlotlyMessage Source code
updateQualityParam Man page
updateQualityParam,QualityReport-method Man page
updateQualityParam,SangerAlignment-method Man page
updateQualityParam,SangerContig-method Man page
updateQualityParam,SangerRead-method Man page
valueBoxChromTrimmedFinishPos Source code
valueBoxChromTrimmedStartPos Source code
valueBoxM1TrimmingCutoff Source code
valueBoxM2CutoffQualityScore Source code
valueBoxM2SlidingWindowSize Source code
valueBoxRawMeanQualityScore Source code
valueBoxRawMinQualityScore Source code
valueBoxRawSeqLength Source code
valueBoxRemainingRatio Source code
valueBoxSAAcceptStopCodons Source code
valueBoxSAMaxFractionLost Source code
valueBoxSAMaxFractionLostSA Source code
valueBoxSAMinFractionCall Source code
valueBoxSAMinFractionCallSA Source code
valueBoxSAMinReadLength Source code
valueBoxSAMinReadsNum Source code
valueBoxSAReadingFrame Source code
valueBoxSCAcceptStopCodons Source code
valueBoxSCMaxFractionLost Source code
valueBoxSCMinFractionCall Source code
valueBoxSCMinReadLength Source code
valueBoxSCMinReadsNum Source code
valueBoxSCReadingFrame Source code
valueBoxTrimmedFinishPos Source code
valueBoxTrimmedMeanQualityScore Source code
valueBoxTrimmedMinQualityScore Source code
valueBoxTrimmedSeqLength Source code
valueBoxTrimmedStartPos Source code
vline Source code
writeFasta Man page Source code
writeFastaSA Man page
writeFastaSA,SangerAlignment-method Man page
writeFastaSC Man page
writeFastaSC,SangerContig-method Man page
writeFastaSR Man page
writeFastaSR,SangerRead-method Man page
sangeranalyseR documentation built on Nov. 8, 2020, 5:59 p.m.

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