Package: sangeranalyseR 1.23.0

Kuan-Hao Chao

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

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

Authors:Rob Lanfear [aut], Kuan-Hao Chao [aut, cre]

sangeranalyseR_1.23.0.tar.gz
sangeranalyseR_1.23.0.zip(r-4.7)sangeranalyseR_1.23.0.zip(r-4.6)sangeranalyseR_1.23.0.zip(r-4.5)
sangeranalyseR_1.23.0.tgz(r-4.6-x86_64)sangeranalyseR_1.23.0.tgz(r-4.6-arm64)sangeranalyseR_1.23.0.tgz(r-4.5-x86_64)sangeranalyseR_1.23.0.tgz(r-4.5-arm64)
sangeranalyseR_1.23.0.tar.gz(r-4.7-arm64)sangeranalyseR_1.23.0.tar.gz(r-4.7-x86_64)sangeranalyseR_1.23.0.tar.gz(r-4.6-arm64)sangeranalyseR_1.23.0.tar.gz(r-4.6-x86_64)
sangeranalyseR_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
sangeranalyseR/json (API)
NEWS

# Install 'sangeranalyseR' in R:
install.packages('sangeranalyseR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/roblanf/sangeranalyser/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:sangeranalyseR-1.23.0(bioc 3.24)sangeranalyseR-1.22.0(bioc 3.23)

geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationguicpp

8.67 score 104 stars 64 scripts 628 downloads 5 mentions 24 exports 109 dependencies

Last updated from:f6375aed24. Checks:1 WARNING, 13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING207
linux-devel-arm64OK439
linux-devel-x86_64OK465
source / vignettesOK326
linux-release-arm64OK455
linux-release-x86_64OK456
macos-release-arm64OK318
macos-release-x86_64OK557
macos-oldrel-arm64OK260
macos-oldrel-x86_64OK510
windows-develOK937
windows-releaseOK867
windows-oldrelOK979
wasm-releaseOK163

Exports:chromatogram_overwritechromatogram_plotlygenerateReportgenerateReportSAgenerateReportSCgenerateReportSRglobalTrimApplaunchApplaunchAppSAlaunchAppSCMakeBaseCallsprimaryAASeqS1primaryAASeqS2primaryAASeqS3qualityBasePlotreadTableSangerAlignmentSangerContigSangerReadupdateQualityParamwriteFastawriteFastaSAwriteFastaSCwriteFastaSR

Dependencies:ade4apeaskpassbase64encBHBiocGenericsBiocParallelBiostringsbslibcachemclicodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIDECIPHERdigestdplyrDTevaluateexcelRfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggdendroggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecycleloggermagrittrMASSmemoisemimenlmeopensslopenxlsxotelpillarpixmappkgconfigplotlypromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS4VectorsS7sangerseqRsassscalessegmentedSeqinfoseqinrshinyshinycssloadersshinydashboardshinyjsshinyWidgetssnowsourcetoolsspstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableXVectoryamlzip

An Introduction to sangeranalyseR

Kuan-Hao Chao ([email protected])

Rendered fromsangeranalyseR.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-05-06
Started: 2019-12-03

Readme and manuals

Help Manual

Help pageTopics
Static base-R chromatogram renderer with a corrected color palette.chromatogram_overwrite
Render a Sanger chromatogram as an interactive Plotly widgetchromatogram_plotly
ChromatogramParamChromatogramParam-class
Method generateReportgenerateReport
Method generateReportSAgenerateReportSA
Method generateReportSCgenerateReportSC
Method generateReportSRgenerateReportSR
Launch a global trimming controls dashboardglobalTrimApp
Method launchApplaunchApp
Method launchAppSAlaunchAppSA
Method launchAppSClaunchAppSC
Method MakeBaseCallsMakeBaseCalls
ObjectResultsObjectResults-class
Method primaryAASeqS1primaryAASeqS1 primaryAASeqS1,SangerRead-method
Method primaryAASeqS2primaryAASeqS2 primaryAASeqS2,SangerRead-method
Method primaryAASeqS3primaryAASeqS3 primaryAASeqS3,SangerRead-method
Method qualityBasePlotqualityBasePlot
QualityReportQualityReport-class
qualityBasePlotqualityBasePlot,QualityReport-method QualityReport-class-qualityBasePlot
updateQualityParamQualityReport-class-updateQualityParam updateQualityParam,QualityReport-method
QualityReport instancequalityReportData
Method readTablereadTable
SangerAlignmentSangerAlignment
SangerAlignmentSangerAlignment-class
generateReportSAgenerateReportSA,SangerAlignment-method SangerAlignment-class-generateReportSA
launchAppSAlaunchAppSA,SangerAlignment-method SangerAlignment-class-launchAppSA
updateQualityParamSangerAlignment-class-updateQualityParam updateQualityParam,SangerAlignment-method
writeFastaSASangerAlignment-class-writeFastaSA writeFastaSA,SangerAlignment-method
SangerAlignment instancesangerAlignmentData
sangeranalyseR-packagesangeranalyseR
SangerContigSangerContig
SangerContigSangerContig-class
generateReportSCgenerateReportSC,SangerContig-method SangerContig-class-generateReportSC
launchAppSClaunchAppSC,SangerContig-method SangerContig-class-launchAppSC
readTablereadTable,SangerContig-method SangerContig-class-readTable
updateQualityParamSangerContig-class-updateQualityParam updateQualityParam,SangerContig-method
writeFastaSCSangerContig-class-writeFastaSC writeFastaSC,SangerContig-method
SangerContig instancesangerContigData
SangerReadSangerRead
SangerReadSangerRead-class
generateReportSRgenerateReportSR,SangerRead-method SangerRead-class-generateReportSR
MakeBaseCallsMakeBaseCalls,SangerRead-method SangerRead-class-MakeBaseCalls
qualityBasePlotqualityBasePlot,SangerRead-method SangerRead-class-qualityBasePlot
readTablereadTable,SangerRead-method SangerRead-class-readTable
updateQualityParamSangerRead-class-updateQualityParam updateQualityParam,SangerRead-method
writeFastaSRSangerRead-class-writeFastaSR writeFastaSR,SangerRead-method
SangerRead instancesangerReadFData
Method updateQualityParamupdateQualityParam
Method writeFastawriteFasta
Method writeFastaSAwriteFastaSA
Method writeFastaSCwriteFastaSC
Method writeFastaSRwriteFastaSR